Lib.rs

› Keywords #bioinformatics #fastq #genomics #k-mer #fasta-sequence #bio #genome #sam

#fasta

  1. needletail

    FASTX parsing and k-mer methods

    v0.7.2 10K #bioinformatics #fasta #k-mer #fastq

  2. minimap2

    Bindings to libminimap2

    v0.1.31+minimap2.2.30 210 #genomics #bioinformatics #fasta #fastq

  3. seq_io

    Fast FASTA, FASTQ and FASTX parsing

    v0.4.0-alpha.0 4.0K #fastq #fasta #bio

  4. paraseq

    A minimal-copy parser for FASTA and FASTQ files built for paired parallel processing

    v0.4.9 1.2K #fastq #fasta #parser

  5. predictosaurus

    Uncertainty aware haplotype based genomic variant effect prediction

    v0.10.2 #genomics #genomics-variant #effect-prediction #fasta #genomic-data #haplotypes #peptides #tsv #uncertainty #peptide-sequence

  6. orfm

    A pure-Rust port of OrfM - a simple and not slow open reading frame (ORF) caller

    v2.1.1 #fasta #frame #orf #caller #slow #codon #transcript #fastq #gzipped #nucleotide

  7. merkurio

    Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags

    v1.0.2 #k-mer #sam #fasta #fastq #bio

  8. fastx

    reads Fasta and FastQ files with little overhead

    v0.6.1 #bioinformatics #fasta #fastq #sequencing #genome

  9. fastdedup

    A fast and memory-efficient FASTX PCR deduplication tool

    v1.2.1 #bioinformatics #fasta #fastq #pcr

  10. helicase

    SIMD-accelerated library for FASTA/FASTQ parsing and bitpacking

    v0.1.1 #bioinformatics #bit-packing #fasta #fastq #simd

  11. hashfasta

    Very quickly compute hashes for FASTA/FASTQ files considering only the sequence content

    v1.0.0 #bioinformatics #fasta #hash #fastq #sequencing

  12. minimap2-temp

    Bindings to libminimap2

    v0.1.33+minimap2.2.28 190 #bioinformatics #fasta #fastq

  13. sequenceprofiler

    sequence similarity based on identity kmers and all sequence profiling under one rust crate

    v0.4.0 #genome #k-mer #fasta #identity #graphs #jellyfish #profiling #bioinformatics #sam

  14. verify-same-kmer-content

    Verify that an SPSS has the same kmer content as a set of unitigs

    v1.4.1 650 #genomics #k-mer #file-content #verify #fasta #spss #gfa

  15. multiseqex

    Multi-sequence extractor from FASTA using FAI indexing, with parallelism and flexible region input formats

    v0.2.1 #fasta-sequence #fasta #bioinformatics-sequence #bioinformatics #parallel #faidx

  16. chromsize

    just get your chrom sizes

    v0.0.34 #fasta #chromosome #size #genome

  17. alnstats

    A high-performance command-line tool designed to calculate yield and duplicate statistics from BAM, SAM, or CRAM alignment files

    v0.1.1 #statistics #fasta #duplicates #cram #sam #metrics #bam #paired-end #command-line-tool #se

  18. fasta-filter

    Filter a (multi-sequence) FASTA file and output a subset of the records on STDOUT

    v0.2.0 #fasta #stdout #record #output-file #filter

  19. ugv

    Ultra-fast genome viewer for interactive exploration of genomic data

    v0.1.2 #genomics #bam #bioinformatics #viewer #fasta

  20. noodles-fasta

    FASTA format reader and writer

    v0.60.0 8.8K #fasta #reader-writer #bio

  21. kmerust

    A fast, parallel k-mer counter for DNA sequences in FASTA and FASTQ files

    v0.3.2 #genomics #bioinformatics #k-mer #fasta #dna

  22. check_build

    verify a VCF file against hg19 and hg38 references using a streaming, low-memory approach

    v0.4.0 1.2K #vcf #reference #build-tool #verification #fasta #genome #contig #low-memory #auto-download

  23. doiTAG

    doiTAG for sequence DOIs

    v0.3.0 #doitag #doi #sequence #bioinformatics #command #fasta #debugging #gene

  24. genomemask

    mask specific regions of a genome in any format

    v0.0.3 #genome #fasta #mask #2bit

  25. nail

    alignment inference tool

    v0.5.0 #sequence-alignment #inference #fasta #search-query #seed #fasta-sequence #biological-sequence

  26. thaf

    Extracts transcript sequences and gene maps from genome FASTA files using GFF3 annotations

    v0.0.5 #genome #bioinformatics #fasta #gff3 #transcriptome

  27. seqx

    A command-line tool for processing and analyzing biological sequences

    v0.1.2 #fasta #compression #fastq #statistics #search #dedup #sequence-processing #low-memory #biological #tool-for-processing

  28. seq_io_parallel

    A map-reduce style parallel extension to seq_io

    v0.2.1 700 #bioinformatics #fastq #map-reduce #fasta

  29. pairsnp-rs

    Calculate pairwise SNP distances given a multiple sequence alignment

    v0.3.0 #sequence-alignment #distance-matrix #snp #pairwise #calculate #fasta #tsv #input-file

  30. refget-server

    Axum-based GA4GH refget Sequences v2.0.0 and Sequence Collections v1.0.0 server

    v0.1.0 #genomics #bioinformatics #sequence-collection #collection-v1-0 #refget #v2-0 #fasta #ga4gh #hash

  31. seqtkrs

    reimplementation of seqtk, a fast and lightweight tool for processing biological sequences in FASTA/FASTQ format

    v0.1.1 #genomics #fasta-sequence #bioinformatics #bioinformatics-sequence #fasta #fastq

  32. filterx

    A command line tool to filter data by using python-like syntax

    v0.4.1 750 #sam #csv #filter #fastq #fasta #gff #tsv #bed #command-line-tool #python-like

  33. faimm

    Random access to indexed fasta using a mmapped file

    v0.5.1 #indexed-fasta #fasta #fai #indexed #bio

  34. minimap2-sys

    Bindings to libminimap2

    v0.1.30+minimap2.2.30 320 #bioinformatics #fastq #fasta

  35. cyanea-seq

    Sequence I/O and manipulation for the Cyanea bioinformatics ecosystem

    v0.1.0 #bioinformatics #k-mer #fastq #fasta #dna

  36. fakit

    program for fasta file manipulation

    v0.4.0 1.2K #fasta #bio #fasta-sequence #fa

  37. selexqc

    High-performance parallel RNA Capture-SELEX library quality control

    v0.1.0 #bioinformatics #fasta-sequence #bioinformatics-sequence #fasta #fastq #selex

  38. entab

    Record-format file reader

    v0.3.3 600 #compression #file-reader #record-format #fasta #decompression #tsv #file-parser

  39. fxsplit

    split FASTX into N chunks/files/headers

    v0.0.3 #fasta #io #fastq #split

  40. stats_on_gff3_ncbi

    Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc

    v0.1.52 1.8K #bioinformatics #gff3 #fasta

  41. back_to_sequences

    Back to sequences: find the origin of kmers

    v0.8.3 #k-mer #fasta #origin #find #back #fastq #multi-line #gz #percentage #maximal

  42. stats_on_gff3

    Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc. Examples: stats_on_gff3 Homo_sapiens…

    v0.1.26 320 #bioinformatics #gff3 #fasta

  43. prseq

    Rust tools (with Python bindings) for sequence analysis

    v0.0.33 #bioinformatics #sequence-analysis #fastq #fasta

  44. htsgetr

    htsget protocol server implementation in Rust

    v0.1.6 #htsget #genomics #jwt #fasta #bam #bearer-token #local-storage #cram #jwk #bcf

  45. exon-fasta

    reading and writing FASTA files with Exon

    v0.32.4 #bioinformatics #fasta #exon #arrow #proteomics #sql

  46. base_sequence_compression

    compressing and decompressing DNA sequences

    v1.0.0 250 #compression #dna-sequence #fasta #decompressing #wasm #decompression #compressing-and-decompressing

  47. matchbox-cli

    A flexible processor for sequencing reads

    v0.3.2 #sequencing #fasta #fastq #bam #search #edit-distance #trim #fq #mb

  48. nucleaze

    Read filtering using k-mers

    v1.4.2 #k-mer #reference #multi-threading #fasta #filtering #bioinformatics #serialization #unmatched #fastq

  49. bijux-atlas

    Genomics runtime for GFF3/FASTA ingest, immutable dataset artifacts, gene-query APIs, and OpenAPI export

    v0.2.0 #genomics #bioinformatics #fasta #gff3 #gene-query #bio

  50. refget-store

    Sequence storage backends for GA4GH refget: in-memory, FASTA, and memory-mapped

    v0.1.0 #genomics #fasta #sequence-collection #fasta-sequence #hash #bioinformatics #refget #ga4gh #memory-map #indexed-fasta

  51. kseq

    fasta/fastq format parser library

    v0.5.3 #fastq #fasta

  52. sparc

    binding

    v0.2.0 #bindings #k-mer #read #query #consensus #consensus-algorithm #fasta #backbone

  53. tree-sitter-fasta

    Fasta file parser

    v1.0.8 #tree-sitter #fasta #parser

  54. fastlin

    an ultra-fast program for MTBC lineage typing

    v0.4.1 170 #fastq #bam #lineage #fasta #typing

  55. filterx_info

    The builtin function documentation library for filterx

    v0.4.1 410 #filterx #sam #documentation #fastq #fasta #tsv #bed #gff #bioinformatics #csv

  56. seq-events

    A minimal, zero-copy streaming parser for FASTA/FASTQ files

    v0.1.0 #bioinformatics #streaming-parser #fastq #fasta

  57. psdm

    Compute a pairwise SNP distance matrix from one or two alignment(s)

    v0.3.0 120 #bioinformatics #snp #fasta #pairwise #matrix

  58. miniphy

    Create an ordered FASTA TAR file

    v2.0.0-alpha.8 150 #fasta #compression #batch #ordered #tar #genome #phylogenetic

  59. filterx_engine

    The engine library for filterx

    v0.4.1 500 #filterx #fastq #sam #fasta #vcf #tsv #gff #bed #csv #bioinformatics

  60. kira-cdh

    Single-binary, CLI-compatible replacement for CD-HIT utilities (cd-hit, cd-hit-est, cd-hit-2d, cd-hit-est-2d) in Rust

    v0.1.1 #cd-hit #fasta #min-hash #replace #single-binary #k-mer #modes #lsh #cluster-analysis #candidate

  61. deepbiop-fa

    Deep Learning Preprocessing Library for Fastq Format

    v0.1.16 #bioinformatics #deep-learning #fasta #parquet

  62. spillover-bio

    Genomics-focused disk-spilling sort pipeline for FASTQ/FASTA sequence records

    v0.1.3 #record #sorting #fastq #spillover #fasta #fasta-sequence #dedup #dryice #acceleration #sorter

  63. codonrs

    Calculate relative synonymous codon usage for coding DNA sequences in a fasta file

    v0.2.8 #codon #fasta #fasta-sequence #dna-sequence #calculate #dna-sequence-analysis #file-analysis

  64. fasta-cleaner

    Transform fasta files by upper-casing all sequence characters and removing non-ACGT sequence characters

    v1.0.1 #fasta #fasta-sequence #character #removing #input-file #cleaner #upper-case

  65. mmft

    A minimal fasta toolkit

    v0.2.1 180 #fasta #tool

  66. poasta

    Fast, optimal, gap-affine partial order alignment

    v0.1.0 #sequence-alignment #fasta #graph #order-alignment #gap #aligner #penalty

  67. fastleng

    read length statistics tool

    v0.2.0 #length #statistics #fastq #fasta #generator #fastx #metrics #fastx-file #n50 #bam-file

  68. bio-streams

    Streaming bioinformatics data types

    v0.5.0 130 #genomics #bioinformatics #fastq #fasta

  69. libsfasta

    Better FASTA sequence compression and querying

    v0.3.4 #bioinformatics #fasta #compression

  70. seqtk-rs

    sequence processing tool written in Rust for manipulating FASTA/FASTQ files. Pure rust version of seqtk.

    v0.2.0 #bio #fasta-sequence #fasta #fastq #ngs

  71. fasta_windows

    Make quick statistics in windows from a fasta file

    v0.2.4 #genomics #fasta #windows

  72. tca

    A platform for scientific data processing and analysis

    v0.1.1-alpha.4 #data-fusion #bioinformatics #compression #data-analysis #fasta #infer #session-context #exon #extension-traits #scientific-data

  73. filterx_source

    The source library for filterx

    v0.4.1 500 #filterx #fastq #fasta #bioinformatics #format #fasta-vcf

    74. Try searching with DuckDuckGo.

  74. fusta

    leverages the FUSE interface to transparently manipulate multiFASTA files as independent files

    v1.7.1 #fasta #bioinformatics #fuse

  75. tf-binding-rs

    Fast transcription factor binding site prediction and FASTA manipulation in Rust

    v0.1.4 210 #fasta #transcription-factor #bindings #site #dna-sequence #pwm #dna-sequence-analysis #genomics #landscape #occupancy

  76. bamsalvage

    Rust version of bamsalvage, retrieving sequences from a corrupted BAM file as much as possible

    v0.1.3 #bio #long-read #fastq #fasta

  77. nu_plugin_bio

    Parse and manipulate common bioinformatic formats in nushell

    v0.85.0 #bioinformatics #nu-shell #format #fasta #structured-data #parse-and-manipulate

  78. biotest

    Generate random test data for bioinformatics

    v0.2.0 #bioinformatics #random #random-test #random-data #fastq #random-sequence #testing-data #fasta

  79. motif_finder

    Find motifs using Gibbs Sampler, Median String, and Randomized Motif Search algorithms in a fasta formatted file of reads Refer to the README to understand the input data

    v0.9.2 #fasta #search-algorithms #string-algorithm #motifs #finder #motif #gibbs #sampler #input-file #input-data

  80. rust-lib-reference-genome

    Reference genome library for Rust

    v0.2.1 #genome #reference #in-memory #fasta #load

  81. fire-fasta

    Ultra-fast, lazy, zero-copy Multi-FASTA parser

    v0.1.0 #bioinformatics #fasta #parser #bio

  82. fastxgz

    A fasta/fastq parser for both compressed and not compressed files

    v0.4.0 #fastq #fasta #compression #gz #k-mer #fastx #hash

  83. rspoa

    A POA implementation in Rust

    v0.1.0 #poa #fasta #graph-path #alignment #score #gap #gaf #gfa

  84. to-trans

    A high-performance transcriptome builder from fasta + GTF/GFF

    v0.2.0 #gtf-gff #fasta #transcriptome #gtf #gff

  85. rust-parallelfastx

    Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does

    v0.1.1 #bioinformatics #fastq #fasta

  86. miniprot-sys

    Bindings to libminiprot

    v0.1.0 #bioinformatics #fasta-protein #fasta #protein #alignment

  87. filterx_core

    The core library for filterx

    v0.4.1 500 #csv #sam #fastq #fasta #tsv #gff #bed

  88. fasta_split

    Split a fasta file into several fasta files

    v0.1.3 #fasta #bioinformatics

  89. fastx-statistics

    Compute simple statistics for fasta-like files

    v1.0.0 #statistics #compute #fasta #fastq

  90. fasta

    Tools for FASTA reading, writing and indexing

    v0.1.3 #indexing #format #parser #line #command-line-utilities

  91. fffx

    fasta/q/x file format parser. Well fuzzed.

    v0.1.3 240 #bioinformatics #fastq #fasta #compression

  92. fastats

    CLI to generate FASTA file statistics (masking, GC content, etc.)

    v0.1.0 #bioinformatics #fasta #bio

  93. seqdupes

    Compress sequence duplicates

    v0.2.0 #fasta #fastq

  94. fasta-stats

    descriptive statistics on FASTA (biological sequence) data

    v0.3.1 #fasta #biological-sequence #statistics #fasta-sequence #descriptive #biological-data #std-dev

  95. rust-gc-count

    GC and sequence utilities

    v0.1.0 #bio #fasta

  96. jean_io

    I/O library feature for jean

    v0.1.0 #fasta-protein #dna-rna #dna #rna #protein #fasta #gff3

  97. syncmers

    finding syncmers

    v0.1.5 #bioinformatics #bioinformatics-sequence #fasta #fastq #fasta-sequence

  98. faiquery

    Queryable indexed fasta using a mmapped file

    v0.1.3 #fasta #indexed-fasta #fai #indexed

  99. stats_on_genomes

    Calculate 2 simple ratio on the whole genome: GC ratio and repetition ratio

    v0.1.1 #bioinformatics #fasta

  100. select-random-fastx

    Select random entries from fastx files

    v0.1.1 #fasta #fastq #entries #fastx #random

  101. unitig_flipper

    Reorienting unitigs to reduce the number of dummy nodes in an SBWT

    v0.1.0 #dummy #flipper #node #unitigs #numbers #sbwt #fasta #k-mer