reads_filter

May 24, 2025

fastp version: 0.24.1; fastqc version: 0.11.0; multiqc version: 1.29

[3]: fastp -h

option needs value: --html

usage: fastp [options] …
options:
-i, --in1 read1 input file name (string [=])
-o, --out1 read1 output file name (string [=])
-I, --in2 read2 input file name (string [=])
-O, --out2 read2 output file name (string [=])
--unpaired1 for PE input, if read1 passed QC but
read2 not, it will be written to unpaired1. Default is to discard it. (string
[=])
--unpaired2 for PE input, if read2 passed QC but
read1 not, it will be written to unpaired2. If --unpaired2 is same as
--unpaired1 (default mode), both unpaired reads will be written to this same
file. (string [=])
--overlapped_out for each read pair, output the overlapped
region if it has no any mismatched base. (string [=])
--failed_out specify the file to store reads that
cannot pass the filters. (string [=])
-m, --merge for paired-end input, merge each pair of
reads into a single read if they are overlapped. The merged reads will be
written to the file given by --merged_out, the unmerged reads will be written to
the files specified by --out1 and --out2. The merging mode is disabled by
default.
--merged_out in the merging mode, specify the file
name to store merged output, or specify --stdout to stream the merged output
(string [=])
--include_unmerged in the merging mode, write the unmerged
or unpaired reads to the file specified by --merge. Disabled by default.
-6, --phred64 indicate the input is using phred64
scoring (it'll be converted to phred33, so the output will still be phred33)
-z, --compression compression level for gzip output (1 ~
9). 1 is fastest, 9 is smallest, default is 4. (int [=4])
--stdin input from STDIN. If the STDIN is
interleaved paired-end FASTQ, please also add --interleaved_in.

1
 --stdout stream passing-filters reads to STDOUT.
This option will result in interleaved FASTQ output for paired-end output.
Disabled by default.
--interleaved_in indicate that <in1> is an interleaved
FASTQ which contains both read1 and read2. Disabled by default.
--reads_to_process specify how many reads/pairs to be
processed. Default 0 means process all reads. (int [=0])
--dont_overwrite don't overwrite existing files.
Overwritting is allowed by default.
--fix_mgi_id the MGI FASTQ ID format is not compatible
with many BAM operation tools, enable this option to fix it.
-V, --verbose output verbose log information (i.e. when
every 1M reads are processed).
-A, --disable_adapter_trimming adapter trimming is enabled by default.
If this option is specified, adapter trimming is disabled
-a, --adapter_sequence the adapter for read1. For SE data, if
not specified, the adapter will be auto-detected. For PE data, this is used if
R1/R2 are found not overlapped. (string [=auto])
--adapter_sequence_r2 the adapter for read2 (PE data only).
This is used if R1/R2 are found not overlapped. If not specified, it will be the
same as <adapter_sequence> (string [=auto])
--adapter_fasta specify a FASTA file to trim both read1
and read2 (if PE) by all the sequences in this FASTA file (string [=])
--detect_adapter_for_pe by default, the auto-detection for
adapter is for SE data input only, turn on this option to enable it for PE data.
-f, --trim_front1 trimming how many bases in front for
read1, default is 0 (int [=0])
-t, --trim_tail1 trimming how many bases in tail for
read1, default is 0 (int [=0])
-b, --max_len1 if read1 is longer than max_len1, then
trim read1 at its tail to make it as long as max_len1. Default 0 means no
limitation (int [=0])
-F, --trim_front2 trimming how many bases in front for
read2. If it's not specified, it will follow read1's settings (int [=0])
-T, --trim_tail2 trimming how many bases in tail for
read2. If it's not specified, it will follow read1's settings (int [=0])
-B, --max_len2 if read2 is longer than max_len2, then
trim read2 at its tail to make it as long as max_len2. Default 0 means no
limitation. If it's not specified, it will follow read1's settings (int [=0])
-D, --dedup enable deduplication to drop the
duplicated reads/pairs
--dup_calc_accuracy accuracy level to calculate duplication
(1~6), higher level uses more memory (1G, 2G, 4G, 8G, 16G, 24G). Default 1 for
no-dedup mode, and 3 for dedup mode. (int [=0])
--dont_eval_duplication don't evaluate duplication rate to save
time and use less memory.
-g, --trim_poly_g force polyG tail trimming, by default
trimming is automatically enabled for Illumina NextSeq/NovaSeq data

2
 --poly_g_min_len the minimum length to detect polyG in the
read tail. 10 by default. (int [=10])
-G, --disable_trim_poly_g disable polyG tail trimming, by default
trimming is automatically enabled for Illumina NextSeq/NovaSeq data
-x, --trim_poly_x enable polyX trimming in 3' ends.
--poly_x_min_len the minimum length to detect polyX in the
read tail. 10 by default. (int [=10])
-5, --cut_front move a sliding window from front (5') to
tail, drop the bases in the window if its mean quality < threshold, stop
otherwise.
-3, --cut_tail move a sliding window from tail (3') to
front, drop the bases in the window if its mean quality < threshold, stop
otherwise.
-r, --cut_right move a sliding window from front to tail,
if meet one window with mean quality < threshold, drop the bases in the window
and the right part, and then stop.
-W, --cut_window_size the window size option shared by
cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4])
-M, --cut_mean_quality the mean quality requirement option
shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int
[=20])
--cut_front_window_size the window size option of cut_front,
default to cut_window_size if not specified (int [=4])
--cut_front_mean_quality the mean quality requirement option for
cut_front, default to cut_mean_quality if not specified (int [=20])
--cut_tail_window_size the window size option of cut_tail,
default to cut_window_size if not specified (int [=4])
--cut_tail_mean_quality the mean quality requirement option for
cut_tail, default to cut_mean_quality if not specified (int [=20])
--cut_right_window_size the window size option of cut_right,
default to cut_window_size if not specified (int [=4])
--cut_right_mean_quality the mean quality requirement option for
cut_right, default to cut_mean_quality if not specified (int [=20])
-Q, --disable_quality_filtering quality filtering is enabled by default.
If this option is specified, quality filtering is disabled
-q, --qualified_quality_phred the quality value that a base is
qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
-u, --unqualified_percent_limit how many percents of bases are allowed to
be unqualified (0~100). Default 40 means 40% (int [=40])
-n, --n_base_limit if one read's number of N base is
>n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
-e, --average_qual if one read's average quality score
<avg_qual, then this read/pair is discarded. Default 0 means no requirement (int
[=0])
-L, --disable_length_filtering length filtering is enabled by default.
If this option is specified, length filtering is disabled
-l, --length_required reads shorter than length_required will
be discarded, default is 15. (int [=15])

3
 --length_limit reads longer than length_limit will be
discarded, default 0 means no limitation. (int [=0])
-y, --low_complexity_filter enable low complexity filter. The
complexity is defined as the percentage of base that is different from its next
base (base[i] != base[i+1]).
-Y, --complexity_threshold the threshold for low complexity filter
(0~100). Default is 30, which means 30% complexity is required. (int [=30])
--filter_by_index1 specify a file contains a list of
barcodes of index1 to be filtered out, one barcode per line (string [=])
--filter_by_index2 specify a file contains a list of
barcodes of index2 to be filtered out, one barcode per line (string [=])
--filter_by_index_threshold the allowed difference of index barcode
for index filtering, default 0 means completely identical. (int [=0])
-c, --correction enable base correction in overlapped
regions (only for PE data), default is disabled
--overlap_len_require the minimum length to detect overlapped
region of PE reads. This will affect overlap analysis based PE merge, adapter
trimming and correction. 30 by default. (int [=30])
--overlap_diff_limit the maximum number of mismatched bases to
detect overlapped region of PE reads. This will affect overlap analysis based PE
merge, adapter trimming and correction. 5 by default. (int [=5])
--overlap_diff_percent_limit the maximum percentage of mismatched
bases to detect overlapped region of PE reads. This will affect overlap analysis
based PE merge, adapter trimming and correction. Default 20 means 20%. (int
[=20])
-U, --umi enable unique molecular identifier (UMI)
preprocessing
--umi_loc specify the location of UMI, can be
(index1/index2/read1/read2/per_index/per_read, default is none (string [=])
--umi_len if the UMI is in read1/read2, its length
should be provided (int [=0])
--umi_prefix if specified, an underline will be used
to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No
prefix by default (string [=])
--umi_skip if the UMI is in read1/read2, fastp can
skip several bases following UMI, default is 0 (int [=0])
--umi_delim delimiter to use between the read name
and the UMI, default is : (string [=:])
-p, --overrepresentation_analysis enable overrepresented sequence analysis.
-P, --overrepresentation_sampling one in (--overrepresentation_sampling)
reads will be computed for overrepresentation analysis (1~10000), smaller is
slower, default is 20. (int [=20])
-j, --json the json format report file name (string
[=fastp.json])
-h, --html the html format report file name (string
[=fastp.html])
-R, --report_title should be quoted with ' or ", default is
"fastp report" (string [=fastp report])

4
 -w, --thread worker thread number, default is 3 (int
[=3])
-s, --split split output by limiting total split file
number with this option (2~999), a sequential number prefix will be added to
output name ( 0001.out.fq, 0002.out.fq…), disabled by default (int [=0])
-S, --split_by_lines split output by limiting lines of each
file with this option(>=1000), a sequential number prefix will be added to
output name ( 0001.out.fq, 0002.out.fq…), disabled by default (long [=0])
-d, --split_prefix_digits the digits for the sequential number
padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to
disable padding (int [=4])
--cut_by_quality5 DEPRECATED, use --cut_front instead.
--cut_by_quality3 DEPRECATED, use --cut_tail instead.
--cut_by_quality_aggressive DEPRECATED, use --cut_right instead.
--discard_unmerged DEPRECATED, no effect now, see the
introduction for merging.
-?, --help print this message

[1]: ls

fastqc_results VA1832-2021
VA2041-2021 VA2095-2021 VA542-2022
fastqc_trimming VA1833-2021
VA2042-2021 VA3232-2021 VA543-2022
skesa_assemblies.ipynb VA1842-2021 VA2043-2021
VA4087-2021
VA1638-2021 VA1887-2021
VA2092-2021 VA4090-2021
VA1701-2021 VA2040-2021
VA2093-2021 VA541-2022

[2]: cd VA1638-2021

[3]: ls

VA1638-2021_S3_L001_R1_001.fastq.gz
VA1638-2021_S3_L001_R2_001.fastq.gz

[4]: fastp -i VA1638-2021_S3_L001_R1_001.fastq.gz -o VA1638-2021_trimmed_R1_001.

↪fastq.gz -I VA1638-2021_S3_L001_R2_001.fastq.gz -O␣

↪VA1638-2021_trimmed_R2_001.fastq.gz -t 3 -T 3 -f 21 -F 21 -w 16

Read1 before filtering:

total reads: 1612419
total bases: 385216491
Q20 bases: 355237753(92.2177%)

5
 Q30 bases: 338487695(87.8695%)

Read2 before filtering:

total reads: 1612419
total bases: 388315698
Q20 bases: 265429810(68.3541%)
Q30 bases: 217240910(55.9444%)

Read1 after filtering:

total reads: 1301600
total bases: 277000395
Q20 bases: 261080908(94.2529%)
Q30 bases: 251441811(90.7731%)

Read2 after filtering:

total reads: 1301600
total bases: 277376191
Q20 bases: 207727855(74.8903%)
Q30 bases: 175905196(63.4176%)

Filtering result:
reads passed filter: 2603200
reads failed due to low quality: 620634
reads failed due to too many N: 0
reads failed due to too short: 1004
reads with adapter trimmed: 542752
bases trimmed due to adapters: 2754504

Duplication rate: 0.123355%

Insert size peak (evaluated by paired-end reads): 353

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA1638-2021_S3_L001_R1_001.fastq.gz -o
VA1638-2021_trimmed_R1_001.fastq.gz -I VA1638-2021_S3_L001_R2_001.fastq.gz -O
VA1638-2021_trimmed_R2_001.fastq.gz -t 3 -T 3 -f 21 -F 21 -w 16
fastp v0.24.1, time used: 15 seconds

[5]: ls

fastp.html
VA1638-2021_S3_L001_R2_001.fastq.gz
fastp.json
VA1638-2021_trimmed_R1_001.fastq.gz
VA1638-2021_S3_L001_R1_001.fastq.gz
VA1638-2021_trimmed_R2_001.fastq.gz

6
[6]: cd ../VA1701-2021

[10]: ls

VA1701-2021_S4_L001_R1_001.fastq.gz
VA1701-2021_S4_L001_R2_001.fastq.gz

[11]: fastp -i VA1701-2021_S4_L001_R1_001.fastq.gz -o VA1701-2021_trimmed_R1_001.

↪fastq.gz -I VA1701-2021_S4_L001_R2_001.fastq.gz -O␣

↪VA1701-2021_trimmed_R2_001.fastq.gz -t 4 -T 4 -f 21 -F 21 -w 16

Read1 before filtering:

total reads: 1649770
total bases: 389185731
Q20 bases: 359553679(92.3861%)
Q30 bases: 342907893(88.1091%)

Read2 before filtering:

total reads: 1649770
total bases: 391679759
Q20 bases: 291890251(74.5227%)
Q30 bases: 248156493(63.357%)

Read1 after filtering:

total reads: 1429765
total bases: 299156897
Q20 bases: 281179984(93.9908%)
Q30 bases: 270299630(90.3538%)

Read2 after filtering:

total reads: 1429765
total bases: 299498792
Q20 bases: 238364662(79.5879%)
Q30 bases: 207475253(69.2742%)

Filtering result:
reads passed filter: 2859530
reads failed due to low quality: 438240
reads failed due to too many N: 0
reads failed due to too short: 1770
reads with adapter trimmed: 617114
bases trimmed due to adapters: 2440871

Duplication rate: 0.158628%

Insert size peak (evaluated by paired-end reads): 390

JSON report: fastp.json

7
 HTML report: fastp.html

fastp -i VA1701-2021_S4_L001_R1_001.fastq.gz -o
VA1701-2021_trimmed_R1_001.fastq.gz -I VA1701-2021_S4_L001_R2_001.fastq.gz -O
VA1701-2021_trimmed_R2_001.fastq.gz -t 4 -T 4 -f 21 -F 21 -w 16
fastp v0.24.1, time used: 16 seconds

[12]: ls

fastp.html
VA1701-2021_S4_L001_R2_001.fastq.gz
fastp.json
VA1701-2021_trimmed_R1_001.fastq.gz
VA1701-2021_S4_L001_R1_001.fastq.gz
VA1701-2021_trimmed_R2_001.fastq.gz

[13]: cd ../VA1832-2021

[16]: ls

VA1832-2021_S5_L001_R1_001.fastq.gz
VA1832-2021_S5_L001_R2_001.fastq.gz

[17]: fastp -i VA1832-2021_S5_L001_R1_001.fastq.gz -o VA1832-2021_trimmed_R1_001.

↪fastq.gz -I VA1832-2021_S5_L001_R2_001.fastq.gz -O␣

↪VA1832-2021_trimmed_R2_001.fastq.gz -t 4 -T 4 -f 21 -F 21 -w 16

Read1 before filtering:

total reads: 2700870
total bases: 635812669
Q20 bases: 589029622(92.642%)
Q30 bases: 562684825(88.4985%)

Read2 before filtering:

total reads: 2700870
total bases: 640160850
Q20 bases: 511233652(79.8602%)
Q30 bases: 448432799(70.05%)

Read1 after filtering:

total reads: 2454906
total bases: 513899596
Q20 bases: 482158793(93.8235%)
Q30 bases: 463083394(90.1116%)

Read2 after filtering:

total reads: 2454906
total bases: 514650854

8
 Q20 bases: 429595266(83.4731%)
Q30 bases: 382325264(74.2883%)

Filtering result:
reads passed filter: 4909812
reads failed due to low quality: 489712
reads failed due to too many N: 0
reads failed due to too short: 2216
reads with adapter trimmed: 1332290
bases trimmed due to adapters: 4226519

Duplication rate: 0.351516%

Insert size peak (evaluated by paired-end reads): 330

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA1832-2021_S5_L001_R1_001.fastq.gz -o
VA1832-2021_trimmed_R1_001.fastq.gz -I VA1832-2021_S5_L001_R2_001.fastq.gz -O
VA1832-2021_trimmed_R2_001.fastq.gz -t 4 -T 4 -f 21 -F 21 -w 16
fastp v0.24.1, time used: 27 seconds

[4]: cd ../VA1833-2021

[5]: ls

VA1833-2021_S6_L001_R1_001.fastq.gz
VA1833-2021_S6_L001_R2_001.fastq.gz

[6]: fastp -i VA1833-2021_S6_L001_R1_001.fastq.gz -o VA1833-2021_trimmed_R1_001.

↪fastq.gz -I VA1833-2021_S6_L001_R2_001.fastq.gz -O␣

↪VA1833-2021_trimmed_R2_001.fastq.gz -t 2 -T 2 -f 20 -F 20 -w 16

Read1 before filtering:

total reads: 2393206
total bases: 553598254
Q20 bases: 512921245(92.6523%)
Q30 bases: 490158775(88.5405%)

Read2 before filtering:

total reads: 2393206
total bases: 561963857
Q20 bases: 368023573(65.4888%)
Q30 bases: 296716775(52.8%)

Read1 after filtering:

total reads: 1880503

9
 total bases: 386657672
Q20 bases: 366630140(94.8203%)
Q30 bases: 354444014(91.6687%)

Read2 after filtering:

total reads: 1880503
total bases: 387569951
Q20 bases: 282351663(72.8518%)
Q30 bases: 237290815(61.2253%)

Filtering result:
reads passed filter: 3761006
reads failed due to low quality: 1023640
reads failed due to too many N: 0
reads failed due to too short: 1766
reads with adapter trimmed: 1187252
bases trimmed due to adapters: 6733581

Duplication rate: 0.155189%

Insert size peak (evaluated by paired-end reads): 242

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA1833-2021_S6_L001_R1_001.fastq.gz -o
VA1833-2021_trimmed_R1_001.fastq.gz -I VA1833-2021_S6_L001_R2_001.fastq.gz -O
VA1833-2021_trimmed_R2_001.fastq.gz -t 2 -T 2 -f 20 -F 20 -w 16
fastp v0.24.1, time used: 21 seconds

[7]: cd ../VA1842-2021

[8]: ls

VA1842-2021_S7_L001_R1_001.fastq.gz
VA1842-2021_S7_L001_R2_001.fastq.gz

[12]: fastp -i VA1842-2021_S7_L001_R1_001.fastq.gz -o VA1842-2021_trimmed_R1_001.

↪fastq.gz -I VA1842-2021_S7_L001_R2_001.fastq.gz -O␣

↪VA1842-2021_trimmed_R2_001.fastq.gz -t 2 -T 2 -f 20 -F 20 -w 16

Read1 before filtering:

total reads: 1180436
total bases: 271645038
Q20 bases: 250923780(92.3719%)
Q30 bases: 239435537(88.1428%)

Read2 before filtering:

10
 total reads: 1180436
total bases: 273271603
Q20 bases: 220349001(80.6337%)
Q30 bases: 194221055(71.0725%)

Read1 after filtering:

total reads: 1073571
total bases: 221933964
Q20 bases: 207582421(93.5334%)
Q30 bases: 199046885(89.6874%)

Read2 after filtering:

total reads: 1073571
total bases: 222118352
Q20 bases: 186786705(84.0933%)
Q30 bases: 166769866(75.0815%)

Filtering result:
reads passed filter: 2147142
reads failed due to low quality: 212462
reads failed due to too many N: 0
reads failed due to too short: 1268
reads with adapter trimmed: 541744
bases trimmed due to adapters: 1799333

Duplication rate: 0.247875%

Insert size peak (evaluated by paired-end reads): 198

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA1842-2021_S7_L001_R1_001.fastq.gz -o
VA1842-2021_trimmed_R1_001.fastq.gz -I VA1842-2021_S7_L001_R2_001.fastq.gz -O
VA1842-2021_trimmed_R2_001.fastq.gz -t 2 -T 2 -f 20 -F 20 -w 16
fastp v0.24.1, time used: 12 seconds

[13]: cd ../VA1887-2021

[14]: ls

VA1887-2021_S8_L001_R1_001.fastq.gz
VA1887-2021_S8_L001_R2_001.fastq.gz

[15]: fastp -i VA1887-2021_S8_L001_R1_001.fastq.gz -o VA1887-2021_trimmed_R1_001.

↪fastq.gz -I VA1887-2021_S8_L001_R2_001.fastq.gz -O␣

↪VA1887-2021_trimmed_R2_001.fastq.gz -t 2 -T 2 -f 20 -F 20 -w 16

11
 Read1 before filtering:
total reads: 2624018
total bases: 613320531
Q20 bases: 566930291(92.4362%)
Q30 bases: 540969342(88.2034%)

Read2 before filtering:

total reads: 2624018
total bases: 616990567
Q20 bases: 509966753(82.6539%)
Q30 bases: 453926494(73.5711%)

Read1 after filtering:

total reads: 2421082
total bases: 510125170
Q20 bases: 476515554(93.4115%)
Q30 bases: 456444734(89.477%)

Read2 after filtering:

total reads: 2421082
total bases: 510614539
Q20 bases: 437175630(85.6175%)
Q30 bases: 393252543(77.0155%)

Filtering result:
reads passed filter: 4842164
reads failed due to low quality: 404348
reads failed due to too many N: 0
reads failed due to too short: 1524
reads with adapter trimmed: 1352518
bases trimmed due to adapters: 4118103

Duplication rate: 0.38826%

Insert size peak (evaluated by paired-end reads): 302

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA1887-2021_S8_L001_R1_001.fastq.gz -o
VA1887-2021_trimmed_R1_001.fastq.gz -I VA1887-2021_S8_L001_R2_001.fastq.gz -O
VA1887-2021_trimmed_R2_001.fastq.gz -t 2 -T 2 -f 20 -F 20 -w 16
fastp v0.24.1, time used: 25 seconds

[16]: cd ../VA2040-2021

[17]: ls

12
 VA2040-2021_S9_L001_R1_001.fastq.gz
VA2040-2021_S9_L001_R2_001.fastq.gz

[18]: fastp -i VA2040-2021_S9_L001_R1_001.fastq.gz -o VA2040-2021_S9_trimmed_001.

↪fastq.gz -I VA2040-2021_S9_L001_R2_001.fastq.gz -O␣

↪VA2040-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 2 -T 2 -w 16

Read1 before filtering:

total reads: 1563938
total bases: 365218631
Q20 bases: 337653666(92.4525%)
Q30 bases: 322345942(88.2611%)

Read2 before filtering:

total reads: 1563938
total bases: 367683729
Q20 bases: 288788727(78.5427%)
Q30 bases: 251463502(68.3913%)

Read1 after filtering:

total reads: 1405667
total bases: 295382844
Q20 bases: 276777783(93.7014%)
Q30 bases: 265690260(89.9478%)

Read2 after filtering:

total reads: 1405667
total bases: 295658774
Q20 bases: 243500821(82.3587%)
Q30 bases: 215293598(72.8183%)

Filtering result:
reads passed filter: 2811334
reads failed due to low quality: 315550
reads failed due to too many N: 0
reads failed due to too short: 992
reads with adapter trimmed: 708540
bases trimmed due to adapters: 2559243

Duplication rate: 0.18511%

Insert size peak (evaluated by paired-end reads): 338

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2040-2021_S9_L001_R1_001.fastq.gz -o
VA2040-2021_S9_trimmed_001.fastq.gz -I VA2040-2021_S9_L001_R2_001.fastq.gz -O

13
 VA2040-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 2 -T 2 -w 16
fastp v0.24.1, time used: 16 seconds

[19]: cd ../VA2041-2021

[20]: ls

VA2041-2021_S10_L001_R1_001.fastq.gz
VA2041-2021_S10_L001_R2_001.fastq.gz

[21]: fastp -i VA2041-2021_S10_L001_R1_001.fastq.gz -o VA2041-2021_trimmed_R1_001.

↪fastq.gz -I VA2041-2021_S10_L001_R2_001.fastq.gz -O␣

↪VA2041-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 2 -T 2 -w 16

Read1 before filtering:

total reads: 2101307
total bases: 494930621
Q20 bases: 457430335(92.4231%)
Q30 bases: 436285000(88.1507%)

Read2 before filtering:

total reads: 2101307
total bases: 499276413
Q20 bases: 361846304(72.4741%)
Q30 bases: 303782694(60.8446%)

Read1 after filtering:

total reads: 1779039
total bases: 376344731
Q20 bases: 354430884(94.1772%)
Q30 bases: 340947286(90.5944%)

Read2 after filtering:

total reads: 1779039
total bases: 376808179
Q20 bases: 293480424(77.8859%)
Q30 bases: 252703553(67.0642%)

Filtering result:
reads passed filter: 3558078
reads failed due to low quality: 643304
reads failed due to too many N: 0
reads failed due to too short: 1232
reads with adapter trimmed: 904258
bases trimmed due to adapters: 4066578

Duplication rate: 0.130871%

14
 Insert size peak (evaluated by paired-end reads): 330

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2041-2021_S10_L001_R1_001.fastq.gz -o
VA2041-2021_trimmed_R1_001.fastq.gz -I VA2041-2021_S10_L001_R2_001.fastq.gz -O
VA2041-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 2 -T 2 -w 16
fastp v0.24.1, time used: 20 seconds

[22]: cd ../VA2042-2021

[23]: ls

VA2042-2021_S1_L001_R1_001.fastq.gz
VA2042-2021_S1_L001_R2_001.fastq.gz

[24]: fastp -i VA2042-2021_S1_L001_R1_001.fastq.gz -o VA2042-2021_trimmed_R1_001.

↪fastq.gz -I VA2042-2021_S1_L001_R2_001.fastq.gz -O␣

↪VA2042-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 2 -T 2 -w 16

Read1 before filtering:

total reads: 2505223
total bases: 593891171
Q20 bases: 548903083(92.4249%)
Q30 bases: 523454552(88.1398%)

Read2 before filtering:

total reads: 2505223
total bases: 597373758
Q20 bases: 475732063(79.6373%)
Q30 bases: 416417051(69.708%)

Read1 after filtering:

total reads: 2261313
total bases: 483819789
Q20 bases: 452981659(93.6261%)
Q30 bases: 434227302(89.7498%)

Read2 after filtering:

total reads: 2261313
total bases: 484264198
Q20 bases: 402865127(83.1912%)
Q30 bases: 357360291(73.7945%)

Filtering result:
reads passed filter: 4522626
reads failed due to low quality: 486762

15
 reads failed due to too many N: 0
reads failed due to too short: 1058
reads with adapter trimmed: 1083528
bases trimmed due to adapters: 3696114

Duplication rate: 0.21559%

Insert size peak (evaluated by paired-end reads): 355

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2042-2021_S1_L001_R1_001.fastq.gz -o
VA2042-2021_trimmed_R1_001.fastq.gz -I VA2042-2021_S1_L001_R2_001.fastq.gz -O
VA2042-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 2 -T 2 -w 16
fastp v0.24.1, time used: 25 seconds

[2]: cd VA2043-2021/

[3]: ls

VA2043-2021_S2_L001_R1_001.fastq.gz
VA2043-2021_S2_L001_R2_001.fastq.gz

[4]: fastp -i VA2043-2021_S2_L001_R1_001.fastq.gz -o VA2043-2021_trimmed_R1_001.

↪fastq.gz -I VA2043-2021_S2_L001_R2_001.fastq.gz -O␣

↪VA2043-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 3 -T 2 -w 16

Read1 before filtering:

total reads: 1696591
total bases: 399749309
Q20 bases: 370112274(92.5861%)
Q30 bases: 353614632(88.4591%)

Read2 before filtering:

total reads: 1696591
total bases: 403031145
Q20 bases: 286219215(71.0166%)
Q30 bases: 238921838(59.2812%)

Read1 after filtering:

total reads: 1424642
total bases: 299860257
Q20 bases: 282956525(94.3628%)
Q30 bases: 272856911(90.9947%)

Read2 after filtering:

total reads: 1424642

16
 total bases: 301630509
Q20 bases: 231189257(76.6465%)
Q30 bases: 198357439(65.7617%)

Filtering result:
reads passed filter: 2849284
reads failed due to low quality: 542520
reads failed due to too many N: 0
reads failed due to too short: 1378
reads with adapter trimmed: 672104
bases trimmed due to adapters: 3100420

Duplication rate: 0.152305%

Insert size peak (evaluated by paired-end reads): 346

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2043-2021_S2_L001_R1_001.fastq.gz -o
VA2043-2021_trimmed_R1_001.fastq.gz -I VA2043-2021_S2_L001_R2_001.fastq.gz -O
VA2043-2021_trimmed_R2_001.fastq.gz -f 20 -F 20 -t 3 -T 2 -w 16
fastp v0.24.1, time used: 16 seconds

[5]: cd ../VA2092-2021

[6]: ls

VA2092-2021-2_S2_L001_R1_001.fastq.gz
VA2092-2021_S1_L001_R1_001.fastq.gz
VA2092-2021-2_S2_L001_R2_001.fastq.gz
VA2092-2021_S1_L001_R2_001.fastq.gz
En este caso, como son varias lecturas R1 y R2, haremos los cortes de calidad con fastp, y luego
“cat” para unir todas las R1 y todas las R2, en sus respectivos archivos.
[8]: fastp -i VA2092-2021-2_S2_L001_R1_001.fastq.gz -o␣
↪VA2092-2021-2_S2_trimmed_R1_001.fastq.gz -I VA2092-2021-2_S2_L001_R2_001.

↪fastq.gz -O VA2092-2021-2_S2_trimmed_R2_001.fastq.gz -f 20 -F 20 -T 1 -t 1␣

↪-w 16

Read1 before filtering:

total reads: 1222381
total bases: 306817631
Q20 bases: 281849161(91.8621%)
Q30 bases: 270886390(88.2891%)

Read2 before filtering:

17
 total reads: 1222381
total bases: 306817631
Q20 bases: 262289307(85.487%)
Q30 bases: 243888111(79.4896%)

Read1 after filtering:

total reads: 1166264
total bases: 243998145
Q20 bases: 230570567(94.4969%)
Q30 bases: 223736861(91.6961%)

Read2 after filtering:

total reads: 1166264
total bases: 243998145
Q20 bases: 218648435(89.6107%)
Q30 bases: 206352067(84.5712%)

Filtering result:
reads passed filter: 2332528
reads failed due to low quality: 112234
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 670326
bases trimmed due to adapters: 48590492

Duplication rate: 1.28315%

Insert size peak (evaluated by paired-end reads): 326

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2092-2021-2_S2_L001_R1_001.fastq.gz -o
VA2092-2021-2_S2_trimmed_R1_001.fastq.gz -I
VA2092-2021-2_S2_L001_R2_001.fastq.gz -O
VA2092-2021-2_S2_trimmed_R2_001.fastq.gz -f 20 -F 20 -T 1 -t 1 -w 16
fastp v0.24.1, time used: 13 seconds

[9]: ls

fastp.html
VA2092-2021-2_S2_trimmed_R1_001.fastq.gz
fastp.json
VA2092-2021-2_S2_trimmed_R2_001.fastq.gz
VA2092-2021-2_S2_L001_R1_001.fastq.gz
VA2092-2021_S1_L001_R1_001.fastq.gz
VA2092-2021-2_S2_L001_R2_001.fastq.gz
VA2092-2021_S1_L001_R2_001.fastq.gz

18
[10]: fastp -i VA2092-2021_S1_L001_R1_001.fastq.gz -o VA2092-2021_S1_trimmed_R1_001.
↪fastq.gz -I VA2092-2021_S1_L001_R2_001.fastq.gz -O␣

↪VA2092-2021_S1_trimmed_R2_001.fastq.gz -f 29 -F 21 -t 1 -T 1 -w 16

Read1 before filtering:

total reads: 1314248
total bases: 329876248
Q20 bases: 306158195(92.81%)
Q30 bases: 295110500(89.461%)

Read2 before filtering:

total reads: 1314248
total bases: 329876248
Q20 bases: 285377612(86.5105%)
Q30 bases: 266861556(80.8975%)

Read1 after filtering:

total reads: 1255506
total bases: 256798012
Q20 bases: 243122683(94.6747%)
Q30 bases: 235867507(91.8494%)

Read2 after filtering:

total reads: 1255506
total bases: 266842060
Q20 bases: 240440573(90.1059%)
Q30 bases: 227519177(85.2636%)

Filtering result:
reads passed filter: 2511012
reads failed due to low quality: 117484
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 695548
bases trimmed due to adapters: 41471124

Duplication rate: 1.25296%

Insert size peak (evaluated by paired-end reads): 271

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2092-2021_S1_L001_R1_001.fastq.gz -o
VA2092-2021_S1_trimmed_R1_001.fastq.gz -I VA2092-2021_S1_L001_R2_001.fastq.gz -O
VA2092-2021_S1_trimmed_R2_001.fastq.gz -f 29 -F 21 -t 1 -T 1 -w 16
fastp v0.24.1, time used: 14 seconds

19
[11]: ls

fastp.html
fastp.json
VA2092-2021-2_S2_L001_R1_001.fastq.gz
VA2092-2021-2_S2_L001_R2_001.fastq.gz
VA2092-2021-2_S2_trimmed_R1_001.fastq.gz
VA2092-2021-2_S2_trimmed_R2_001.fastq.gz
VA2092-2021_S1_L001_R1_001.fastq.gz
VA2092-2021_S1_L001_R2_001.fastq.gz
VA2092-2021_S1_trimmed_R1_001.fastq.gz
VA2092-2021_S1_trimmed_R2_001.fastq.gz

[12]: cd ../VA2093-2021

[13]: ls

VA2093-2021-2_S4_L001_R1_001.fastq.gz
VA2093-2021_S3_L001_R1_001.fastq.gz
VA2093-2021-2_S4_L001_R2_001.fastq.gz
VA2093-2021_S3_L001_R2_001.fastq.gz

[14]: fastp -i VA2093-2021-2_S4_L001_R1_001.fastq.gz -o␣

↪VA2093-2021-2_S4_trimmed_R1_001.fastq.gz -I VA2093-2021-2_S4_L001_R2_001.

↪fastq.gz -O VA2093-2021-2_S4_trimmed_R2_001.fastq.gz -f 21 -F 20 -t 1 -T 1␣

↪-w 16

Read1 before filtering:

total reads: 1289794
total bases: 323738294
Q20 bases: 298751919(92.2819%)
Q30 bases: 287465473(88.7956%)

Read2 before filtering:

total reads: 1289794
total bases: 323738294
Q20 bases: 269694857(83.3064%)
Q30 bases: 247299978(76.3889%)

Read1 after filtering:

total reads: 1215673
total bases: 256077445
Q20 bases: 242640299(94.7527%)
Q30 bases: 235574975(91.9936%)

Read2 after filtering:

total reads: 1215673
total bases: 257293118

20
 Q20 bases: 224750643(87.352%)
Q30 bases: 209136476(81.2834%)

Filtering result:
reads passed filter: 2431346
reads failed due to low quality: 148242
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 658818
bases trimmed due to adapters: 44733442

Duplication rate: 1.24446%

Insert size peak (evaluated by paired-end reads): 270

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2093-2021-2_S4_L001_R1_001.fastq.gz -o
VA2093-2021-2_S4_trimmed_R1_001.fastq.gz -I
VA2093-2021-2_S4_L001_R2_001.fastq.gz -O
VA2093-2021-2_S4_trimmed_R2_001.fastq.gz -f 21 -F 20 -t 1 -T 1 -w 16
fastp v0.24.1, time used: 14 seconds

[17]: cd ../VA2095-2021

[18]: ls

VA2095-2021-2_S6_L001_R1_001.fastq.gz
VA2095-2021_S5_L001_R1_001.fastq.gz
VA2095-2021-2_S6_L001_R2_001.fastq.gz
VA2095-2021_S5_L001_R2_001.fastq.gz

[19]: fastp -i VA2095-2021-2_S6_L001_R1_001.fastq.gz -o␣

↪VA2095-2021-2_S6_trimmed_R1_001.fastq.gz -I VA2095-2021-2_S6_L001_R2_001.

↪fastq.gz -O VA2095-2021-2_S6_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 2 -T 2␣

↪-w 16

Read1 before filtering:

total reads: 1471735
total bases: 369405485
Q20 bases: 339391104(91.8749%)
Q30 bases: 325724504(88.1753%)

Read2 before filtering:

total reads: 1471735
total bases: 369405485
Q20 bases: 323240660(87.5029%)

21
 Q30 bases: 303304491(82.1061%)

Read1 after filtering:

total reads: 1410741
total bases: 296128606
Q20 bases: 279249472(94.3001%)
Q30 bases: 270298793(91.2775%)

Read2 after filtering:

total reads: 1410741
total bases: 296128606
Q20 bases: 270478658(91.3382%)
Q30 bases: 257217242(86.86%)

Filtering result:
reads passed filter: 2821482
reads failed due to low quality: 121988
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 744196
bases trimmed due to adapters: 51151414

Duplication rate: 1.25722%

Insert size peak (evaluated by paired-end reads): 334

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2095-2021-2_S6_L001_R1_001.fastq.gz -o
VA2095-2021-2_S6_trimmed_R1_001.fastq.gz -I
VA2095-2021-2_S6_L001_R2_001.fastq.gz -O
VA2095-2021-2_S6_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 2 -T 2 -w 16
fastp v0.24.1, time used: 16 seconds

[20]: fastp -i VA2095-2021_S5_L001_R1_001.fastq.gz -o VA2095-2021_S5_trimmed_R1_001.

↪fastq.gz -I VA2095-2021_S5_L001_R2_001.fastq.gz -O␣

↪VA2095-2021_S5_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 2 -T 2 -w 16

Read1 before filtering:

total reads: 1544771
total bases: 387737521
Q20 bases: 359179805(92.6348%)
Q30 bases: 346280566(89.308%)

Read2 before filtering:

total reads: 1544771
total bases: 387737521

22
 Q20 bases: 292103599(75.3354%)
Q30 bases: 256014729(66.0278%)

Read1 after filtering:

total reads: 1380094
total bases: 289232821
Q20 bases: 275690668(95.3179%)
Q30 bases: 268789723(92.932%)

Read2 after filtering:

total reads: 1380094
total bases: 289232821
Q20 bases: 234025182(80.9124%)
Q30 bases: 210350491(72.727%)

Filtering result:
reads passed filter: 2760188
reads failed due to low quality: 329354
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 731530
bases trimmed due to adapters: 51053894

Duplication rate: 0.642037%

Insert size peak (evaluated by paired-end reads): 353

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA2095-2021_S5_L001_R1_001.fastq.gz -o
VA2095-2021_S5_trimmed_R1_001.fastq.gz -I VA2095-2021_S5_L001_R2_001.fastq.gz -O
VA2095-2021_S5_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 2 -T 2 -w 16
fastp v0.24.1, time used: 16 seconds

[21]: cd ../VA3232-2021

[22]: ls

VA3232-2021_S5_L001_R1_001.fastq.gz
VA3232-2021_S5_L001_R2_001.fastq.gz

[24]: fastp -i VA3232-2021_S5_L001_R1_001.fastq.gz -o VA3232-2021_trimmed_R1_001.

↪fastq.gz -I VA3232-2021_S5_L001_R2_001.fastq.gz -O␣

↪VA3232-2021_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 4 -w 16

Read1 before filtering:

total reads: 1880186

23
 total bases: 301026002
Q20 bases: 284821156(94.6168%)
Q30 bases: 277725348(92.2596%)

Read2 before filtering:

total reads: 1880186
total bases: 314195238
Q20 bases: 259970409(82.7417%)
Q30 bases: 240175665(76.4415%)

Read1 after filtering:

total reads: 1788215
total bases: 237816467
Q20 bases: 227675784(95.7359%)
Q30 bases: 223031017(93.7828%)

Read2 after filtering:

total reads: 1788215
total bases: 237584067
Q20 bases: 206358878(86.8572%)
Q30 bases: 193611502(81.4918%)

Filtering result:
reads passed filter: 3576430
reads failed due to low quality: 177416
reads failed due to too many N: 0
reads failed due to too short: 6526
reads with adapter trimmed: 3021114
bases trimmed due to adapters: 13575259

Duplication rate: 7.55468%

Insert size peak (evaluated by paired-end reads): 127

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA3232-2021_S5_L001_R1_001.fastq.gz -o
VA3232-2021_trimmed_R1_001.fastq.gz -I VA3232-2021_S5_L001_R2_001.fastq.gz -O
VA3232-2021_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 4 -w 16
fastp v0.24.1, time used: 16 seconds

[25]: cd ../VA4087-2021

[26]: ls

VA4087-21c3_S1_L001_R1_001.fastq.gz
VA4087-21c4_S2_L001_R1_001.fastq.gz

24
 VA4087-21c3_S1_L001_R2_001.fastq.gz
VA4087-21c4_S2_L001_R2_001.fastq.gz

[27]: fastp -i VA4087-21c3_S1_L001_R1_001.fastq.gz -o VA4087-21c3_S1_trimmed_R1_001.

↪fastq.gz -I VA4087-21c3_S1_L001_R2_001.fastq.gz -O␣

↪VA4087-21c3_S1_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16

Read1 before filtering:

total reads: 2261638
total bases: 286392493
Q20 bases: 280827161(98.0567%)
Q30 bases: 278487190(97.2397%)

Read2 before filtering:

total reads: 2261638
total bases: 286905898
Q20 bases: 276687353(96.4384%)
Q30 bases: 272780943(95.0768%)

Read1 after filtering:

total reads: 2228047
total bases: 230244245
Q20 bases: 226253407(98.2667%)
Q30 bases: 224441797(97.4799%)

Read2 after filtering:

total reads: 2228047
total bases: 230421403
Q20 bases: 223169238(96.8527%)
Q30 bases: 220357381(95.6323%)

Filtering result:
reads passed filter: 4456094
reads failed due to low quality: 50746
reads failed due to too many N: 0
reads failed due to too short: 16436
reads with adapter trimmed: 2291498
bases trimmed due to adapters: 460571

Duplication rate: 2.53812%

Insert size peak (evaluated by paired-end reads): 115

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA4087-21c3_S1_L001_R1_001.fastq.gz -o
VA4087-21c3_S1_trimmed_R1_001.fastq.gz -I VA4087-21c3_S1_L001_R2_001.fastq.gz -O

25
 VA4087-21c3_S1_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16
fastp v0.24.1, time used: 13 seconds

[28]: fastp -i VA4087-21c4_S2_L001_R1_001.fastq.gz -o VA4087-21c4_S2_trimmed_R1_001.

↪fastq.gz -I VA4087-21c4_S2_L001_R2_001.fastq.gz -O␣

↪VA4087-21c4_S2_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16

Read1 before filtering:

total reads: 1979131
total bases: 248493695
Q20 bases: 243787127(98.106%)
Q30 bases: 241827300(97.3173%)

Read2 before filtering:

total reads: 1979131
total bases: 249050374
Q20 bases: 238383799(95.7171%)
Q30 bases: 234514215(94.1634%)

Read1 after filtering:

total reads: 1948060
total bases: 199254019
Q20 bases: 195929953(98.3317%)
Q30 bases: 194429641(97.5788%)

Read2 after filtering:

total reads: 1948060
total bases: 199437762
Q20 bases: 191870868(96.2059%)
Q30 bases: 189123836(94.8285%)

Filtering result:
reads passed filter: 3896120
reads failed due to low quality: 47300
reads failed due to too many N: 0
reads failed due to too short: 14842
reads with adapter trimmed: 2056876
bases trimmed due to adapters: 472512

Duplication rate: 2.89117%

Insert size peak (evaluated by paired-end reads): 115

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA4087-21c4_S2_L001_R1_001.fastq.gz -o
VA4087-21c4_S2_trimmed_R1_001.fastq.gz -I VA4087-21c4_S2_L001_R2_001.fastq.gz -O

26
 VA4087-21c4_S2_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16
fastp v0.24.1, time used: 11 seconds

[29]: cd ../VA4090-2021

[30]: ls

VA4090-21c1_S1_L001_R1_001.fastq.gz
VA4090-21c2_S2_L001_R1_001.fastq.gz
VA4090-21c1_S1_L001_R2_001.fastq.gz
VA4090-21c2_S2_L001_R2_001.fastq.gz

[31]: fastp -i VA4090-21c1_S1_L001_R1_001.fastq.gz -o VA4090-21c1_S1_trimmed_R1_001.

↪fastq.gz -I VA4090-21c1_S1_L001_R2_001.fastq.gz -O␣

↪VA4090-21c1_S1_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16

Read1 before filtering:

total reads: 2231889
total bases: 311650786
Q20 bases: 302287180(96.9955%)
Q30 bases: 298534283(95.7913%)

Read2 before filtering:

total reads: 2231889
total bases: 311884694
Q20 bases: 297520216(95.3943%)
Q30 bases: 291690015(93.525%)

Read1 after filtering:

total reads: 2204585
total bases: 255347625
Q20 bases: 247946213(97.1014%)
Q30 bases: 244990735(95.944%)

Read2 after filtering:

total reads: 2204585
total bases: 255423507
Q20 bases: 244624601(95.7722%)
Q30 bases: 240212066(94.0446%)

Filtering result:
reads passed filter: 4409170
reads failed due to low quality: 49526
reads failed due to too many N: 0
reads failed due to too short: 5082
reads with adapter trimmed: 1662504
bases trimmed due to adapters: 376459

27
 Duplication rate: 2.41226%

Insert size peak (evaluated by paired-end reads): 168

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA4090-21c1_S1_L001_R1_001.fastq.gz -o
VA4090-21c1_S1_trimmed_R1_001.fastq.gz -I VA4090-21c1_S1_L001_R2_001.fastq.gz -O
VA4090-21c1_S1_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16
fastp v0.24.1, time used: 15 seconds

[32]: fastp -i VA4090-21c2_S2_L001_R1_001.fastq.gz -o VA4090-21c2_S2_trimmed_R1_001.

↪fastq.gz -I VA4090-21c2_S2_L001_R2_001.fastq.gz -O␣

↪VA4090-21c2_S2_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16

Read1 before filtering:

total reads: 2497124
total bases: 346642849
Q20 bases: 336827567(97.1685%)
Q30 bases: 332894957(96.034%)

Read2 before filtering:

total reads: 2497124
total bases: 346901294
Q20 bases: 334093828(96.308%)
Q30 bases: 328617894(94.7295%)

Read1 after filtering:

total reads: 2469381
total bases: 283939640
Q20 bases: 276170510(97.2638%)
Q30 bases: 273052207(96.1656%)

Read2 after filtering:

total reads: 2469381
total bases: 284034063
Q20 bases: 274525716(96.6524%)
Q30 bases: 270386338(95.195%)

Filtering result:
reads passed filter: 4938762
reads failed due to low quality: 50150
reads failed due to too many N: 0
reads failed due to too short: 5336
reads with adapter trimmed: 2009198
bases trimmed due to adapters: 416879

28
 Duplication rate: 2.22232%

Insert size peak (evaluated by paired-end reads): 168

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA4090-21c2_S2_L001_R1_001.fastq.gz -o
VA4090-21c2_S2_trimmed_R1_001.fastq.gz -I VA4090-21c2_S2_L001_R2_001.fastq.gz -O
VA4090-21c2_S2_trimmed_R2_001.fastq.gz -f 21 -F 21 -t 3 -T 3 -w 16
fastp v0.24.1, time used: 16 seconds

[34]: cd ../VA541-2022

[35]: ls

VA541-2022-2_R1.fastq.gz VA541-2022-2_R2.fastq.gz
VA541-2022_R1.fastq.gz
VA541-2022.2_R1.fastq.gz VA541-2022.2_R2.fastq.gz
VA541-2022_R2.fastq.gz

[37]: fastp -i VA541-2022-2_R1.fastq.gz -o VA541-2022-2_R1_trimmed.fastq.gz -I␣

↪VA541-2022-2_R2.fastq.gz -O VA541-2022-2_R2_trimmed.fastq.gz -f 21 -F 21 -t␣

↪1 -T 1 -w 16

Read1 before filtering:

total reads: 3670412
total bases: 554232212
Q20 bases: 513916024(92.7258%)
Q30 bases: 481789788(86.9292%)

Read2 before filtering:

total reads: 3670412
total bases: 554232212
Q20 bases: 512294073(92.4331%)
Q30 bases: 470404283(84.8749%)

Read1 after filtering:

total reads: 3424451
total bases: 406365581
Q20 bases: 384954859(94.7312%)
Q30 bases: 361592780(88.9821%)

Read2 after filtering:

total reads: 3424451
total bases: 406696672
Q20 bases: 384679079(94.5862%)
Q30 bases: 353248639(86.858%)

29
 Filtering result:
reads passed filter: 6848902
reads failed due to low quality: 481038
reads failed due to too many N: 3316
reads failed due to too short: 7568
reads with adapter trimmed: 3307802
bases trimmed due to adapters: 69689585

Duplication rate: 2.91678%

Insert size peak (evaluated by paired-end reads): 157

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA541-2022-2_R1.fastq.gz -o VA541-2022-2_R1_trimmed.fastq.gz -I

VA541-2022-2_R2.fastq.gz -O VA541-2022-2_R2_trimmed.fastq.gz -f 21 -F 21 -t 1 -T
1 -w 16
fastp v0.24.1, time used: 21 seconds

[38]: fastp -i VA541-2022.2_R1.fastq.gz -o VA541-2022.2_R1_trimmed.fastq.gz -I␣

↪VA541-2022.2_R2.fastq.gz -O VA541-2022.2_R2_trimmed.fastq.gz -f 21 -F 21 -t␣

↪1 -T 1 -w 16

Read1 before filtering:

total reads: 11351881
total bases: 1714134031
Q20 bases: 1584881393(92.4596%)
Q30 bases: 1484395303(86.5974%)

Read2 before filtering:

total reads: 11351881
total bases: 1714134031
Q20 bases: 1585249947(92.4811%)
Q30 bases: 1454377083(84.8462%)

Read1 after filtering:

total reads: 10596086
total bases: 1256476359
Q20 bases: 1187929529(94.5445%)
Q30 bases: 1114449443(88.6964%)

Read2 after filtering:

total reads: 10596086
total bases: 1257447270
Q20 bases: 1189363428(94.5856%)
Q30 bases: 1091333906(86.7896%)

30
 Filtering result:
reads passed filter: 21192172
reads failed due to low quality: 1478618
reads failed due to too many N: 10298
reads failed due to too short: 22674
reads with adapter trimmed: 10329036
bases trimmed due to adapters: 217609677

Duplication rate: 35.2916%

Insert size peak (evaluated by paired-end reads): 157

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA541-2022.2_R1.fastq.gz -o VA541-2022.2_R1_trimmed.fastq.gz -I

VA541-2022.2_R2.fastq.gz -O VA541-2022.2_R2_trimmed.fastq.gz -f 21 -F 21 -t 1 -T
1 -w 16
fastp v0.24.1, time used: 59 seconds

[40]: fastp -i VA541-2022_R1.fastq.gz -o VA541-2022_R1_trimmed.fastq.gz -I␣

↪VA541-2022_R2.fastq.gz -O VA541-2022_R2_trimmed.fastq.gz -f 21 -F 21 -t 1 -T␣

↪1 -w 16

Read1 before filtering:

total reads: 7681469
total bases: 1159901819
Q20 bases: 1070965369(92.3324%)
Q30 bases: 1002605515(86.4388%)

Read2 before filtering:

total reads: 7681469
total bases: 1159901819
Q20 bases: 1072955874(92.504%)
Q30 bases: 983972800(84.8324%)

Read1 after filtering:

total reads: 7171635
total bases: 850110778
Q20 bases: 802974670(94.4553%)
Q30 bases: 752856663(88.5598%)

Read2 after filtering:

total reads: 7171635
total bases: 850750598
Q20 bases: 804684349(94.5852%)
Q30 bases: 738085267(86.7569%)

31
 Filtering result:
reads passed filter: 14343270
reads failed due to low quality: 997580
reads failed due to too many N: 6982
reads failed due to too short: 15106
reads with adapter trimmed: 7021234
bases trimmed due to adapters: 147920092

Duplication rate: 4.37222%

Insert size peak (evaluated by paired-end reads): 157

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA541-2022_R1.fastq.gz -o VA541-2022_R1_trimmed.fastq.gz -I

VA541-2022_R2.fastq.gz -O VA541-2022_R2_trimmed.fastq.gz -f 21 -F 21 -t 1 -T 1
-w 16
fastp v0.24.1, time used: 40 seconds

[41]: cd ../VA542-2022

[42]: ls

VA542-2022-2_R1.fastq.gz VA542-2022-2_R2.fastq.gz
VA542-2022_R1.fastq.gz
VA542-2022.2_R1.fastq.gz VA542-2022.2_R2.fastq.gz
VA542-2022_R2.fastq.gz

[43]: fastp -i VA542-2022-2_R1.fastq.gz -o VA542-2022-2_R1_trimmed.fastq.gz -I␣

↪VA542-2022-2_R2.fastq.gz -O VA542-2022-2_R2_trimmed.fastq.gz -f 25 -F 25 -t␣

↪1 -T 1 -w 16

Read1 before filtering:

total reads: 2981362
total bases: 450185662
Q20 bases: 414623211(92.1005%)
Q30 bases: 388724397(86.3476%)

Read2 before filtering:

total reads: 2981362
total bases: 450185662
Q20 bases: 415759649(92.3529%)
Q30 bases: 381122722(84.659%)

Read1 after filtering:

total reads: 2772126

32
 total bases: 322117785
Q20 bases: 302971986(94.0563%)
Q30 bases: 283713637(88.0776%)

Read2 after filtering:

total reads: 2772126
total bases: 322295178
Q20 bases: 304074310(94.3465%)
Q30 bases: 278004232(86.2576%)

Filtering result:
reads passed filter: 5544252
reads failed due to low quality: 410706
reads failed due to too many N: 2822
reads failed due to too short: 4944
reads with adapter trimmed: 2683728
bases trimmed due to adapters: 48406330

Duplication rate: 1.75584%

Insert size peak (evaluated by paired-end reads): 157

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA542-2022-2_R1.fastq.gz -o VA542-2022-2_R1_trimmed.fastq.gz -I

VA542-2022-2_R2.fastq.gz -O VA542-2022-2_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T
1 -w 16
fastp v0.24.1, time used: 16 seconds

[44]: fastp -i VA542-2022.2_R1.fastq.gz -o VA542-2022.2_R1_trimmed.fastq.gz -I␣

↪VA542-2022.2_R2.fastq.gz -O VA542-2022.2_R2_trimmed.fastq.gz -f 25 -F 25 -t␣

↪1 -T 1 -w 16

Read1 before filtering:

total reads: 9881653
total bases: 1492129603
Q20 bases: 1376242667(92.2335%)
Q30 bases: 1289788130(86.4394%)

Read2 before filtering:

total reads: 9881653
total bases: 1492129603
Q20 bases: 1378553822(92.3883%)
Q30 bases: 1264530081(84.7467%)

Read1 after filtering:

total reads: 9191765

33
 total bases: 1067991438
Q20 bases: 1005506002(94.1493%)
Q30 bases: 941410401(88.1477%)

Read2 after filtering:

total reads: 9191765
total bases: 1068635924
Q20 bases: 1008551668(94.3775%)
Q30 bases: 922626587(86.3368%)

Filtering result:
reads passed filter: 18383530
reads failed due to low quality: 1352900
reads failed due to too many N: 9410
reads failed due to too short: 17466
reads with adapter trimmed: 8898500
bases trimmed due to adapters: 160485780

Duplication rate: 32.3088%

Insert size peak (evaluated by paired-end reads): 148

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA542-2022.2_R1.fastq.gz -o VA542-2022.2_R1_trimmed.fastq.gz -I

VA542-2022.2_R2.fastq.gz -O VA542-2022.2_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T
1 -w 16
fastp v0.24.1, time used: 51 seconds

[45]: fastp -i VA542-2022_R1.fastq.gz -o VA542-2022_R1_trimmed.fastq.gz -I␣

↪VA542-2022_R2.fastq.gz -O VA542-2022_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T␣

↪1 -w 16

Read1 before filtering:

total reads: 6900291
total bases: 1041943941
Q20 bases: 961619456(92.2909%)
Q30 bases: 901063733(86.4791%)

Read2 before filtering:

total reads: 6900291
total bases: 1041943941
Q20 bases: 962794173(92.4036%)
Q30 bases: 883407359(84.7845%)

Read1 after filtering:

total reads: 6419639

34
 total bases: 745873653
Q20 bases: 702534016(94.1894%)
Q30 bases: 657696764(88.178%)

Read2 after filtering:

total reads: 6419639
total bases: 746340746
Q20 bases: 704477358(94.3908%)
Q30 bases: 644622355(86.3711%)

Filtering result:
reads passed filter: 12839278
reads failed due to low quality: 942194
reads failed due to too many N: 6588
reads failed due to too short: 12522
reads with adapter trimmed: 6214772
bases trimmed due to adapters: 112079450

Duplication rate: 3.06194%

Insert size peak (evaluated by paired-end reads): 157

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA542-2022_R1.fastq.gz -o VA542-2022_R1_trimmed.fastq.gz -I

VA542-2022_R2.fastq.gz -O VA542-2022_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T 1
-w 16
fastp v0.24.1, time used: 36 seconds

[47]: cd ../VA543-2022

[48]: ls

VA543-2022-2_R1.fastq.gz VA543-2022-2_R2.fastq.gz
VA543-2022_R1.fastq.gz
VA543-2022.2_R1.fastq.gz VA543-2022.2_R2.fastq.gz
VA543-2022_R2.fastq.gz

[49]: fastp -i VA543-2022-2_R1.fastq.gz -o VA543-2022-2_R1_trimmed.fastq.gz -I␣

↪VA543-2022-2_R2.fastq.gz -O VA543-2022-2_R2_trimmed.fastq.gz -f 25 -F 25 -t␣

↪1 -T 1 -w 16

Read1 before filtering:

total reads: 2382669
total bases: 359783019
Q20 bases: 331106860(92.0296%)
Q30 bases: 309448585(86.0098%)

35
 Read2 before filtering:
total reads: 2382669
total bases: 359783019
Q20 bases: 330784846(91.9401%)
Q30 bases: 302508577(84.0808%)

Read1 after filtering:

total reads: 2208851
total bases: 256565098
Q20 bases: 241234432(94.0246%)
Q30 bases: 225268615(87.8017%)

Read2 after filtering:

total reads: 2208851
total bases: 256708057
Q20 bases: 241352015(94.0181%)
Q30 bases: 220137871(85.7542%)

Filtering result:
reads passed filter: 4417702
reads failed due to low quality: 340998
reads failed due to too many N: 2198
reads failed due to too short: 4440
reads with adapter trimmed: 2135090
bases trimmed due to adapters: 39061341

Duplication rate: 1.63233%

Insert size peak (evaluated by paired-end reads): 147

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA543-2022-2_R1.fastq.gz -o VA543-2022-2_R1_trimmed.fastq.gz -I

VA543-2022-2_R2.fastq.gz -O VA543-2022-2_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T
1 -w 16
fastp v0.24.1, time used: 13 seconds

[50]: fastp -i VA543-2022.2_R1.fastq.gz -o VA543-2022.2_R1_trimmed.fastq.gz -I␣

↪VA543-2022.2_R2.fastq.gz -O VA543-2022.2_R2_trimmed.fastq.gz -f 25 -F 25 -t␣

↪1 -T 1 -w 16

Read1 before filtering:

total reads: 9056436
total bases: 1367521836
Q20 bases: 1259604172(92.1085%)
Q30 bases: 1178450017(86.1741%)

36
 Read2 before filtering:
total reads: 9056436
total bases: 1367521836
Q20 bases: 1259863586(92.1275%)
Q30 bases: 1153549476(84.3533%)

Read1 after filtering:

total reads: 8407353
total bases: 977152795
Q20 bases: 918959320(94.0446%)
Q30 bases: 858867348(87.8949%)

Read2 after filtering:

total reads: 8407353
total bases: 977732860
Q20 bases: 920977216(94.1952%)
Q30 bases: 840875161(86.0025%)

Filtering result:
reads passed filter: 16814706
reads failed due to low quality: 1273186
reads failed due to too many N: 8256
reads failed due to too short: 16724
reads with adapter trimmed: 8087750
bases trimmed due to adapters: 146753539

Duplication rate: 28.6675%

Insert size peak (evaluated by paired-end reads): 147

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA543-2022.2_R1.fastq.gz -o VA543-2022.2_R1_trimmed.fastq.gz -I

VA543-2022.2_R2.fastq.gz -O VA543-2022.2_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T
1 -w 16
fastp v0.24.1, time used: 47 seconds

[52]: fastp -i VA543-2022_R1.fastq.gz -o VA543-2022_R1_trimmed.fastq.gz -I␣

↪VA543-2022_R2.fastq.gz -O VA543-2022_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T␣

↪1 -w 16

Read1 before filtering:

total reads: 6673767
total bases: 1007738817
Q20 bases: 928497312(92.1367%)
Q30 bases: 869001432(86.2328%)

37
Read2 before filtering:
total reads: 6673767
total bases: 1007738817
Q20 bases: 929078740(92.1944%)
Q30 bases: 851040899(84.4505%)

Read1 after filtering:

total reads: 6198502
total bases: 720587697
Q20 bases: 677724888(94.0517%)
Q30 bases: 633598733(87.9281%)

Read2 after filtering:

total reads: 6198502
total bases: 721024803
Q20 bases: 679625201(94.2582%)
Q30 bases: 620737290(86.091%)

Filtering result:
reads passed filter: 12397004
reads failed due to low quality: 932188
reads failed due to too many N: 6058
reads failed due to too short: 12284
reads with adapter trimmed: 5952660
bases trimmed due to adapters: 107692198

Duplication rate: 3.20032%

Insert size peak (evaluated by paired-end reads): 157

JSON report: fastp.json

HTML report: fastp.html

fastp -i VA543-2022_R1.fastq.gz -o VA543-2022_R1_trimmed.fastq.gz -I

VA543-2022_R2.fastq.gz -O VA543-2022_R2_trimmed.fastq.gz -f 25 -F 25 -t 1 -T 1
-w 16
fastp v0.24.1, time used: 35 seconds
Las multiples lecturas para un aislado no serán concatenadas, debido a que Skesa acepta multiples
archivos de lecturas
Listo.

38