STORM (A Scalable Tool for Merging Paired-End Reads with Variable Insert Sizes)
Original Repository: https://bitbucket.org/yaoornl/align_test
This is STORM version 1.5
- STORM is a tool for merging paired-end reads with variable insert sizes (i.e. for both overlapping and non-overlapping pairs)
- STORM results in longer reads with higher accuracy compared to current popular merging tools
- STORM is also able to remove contained reads or identical reads
- STORM can generate overlap graphs as input of Omega2
https://github.com/qiumingyao/omega2
https://bitbucket.org/omicsbio/omega2
- Download the package
- Go to the Release folder, and "make"
- run "./storm -h"
./storm
Usage: storm [OPTION]...[PARAM]...
[PARAM]
-i/--instance MergePairedEndReads, RemoveContainedReads, ConstructOverlapGraph
-q/--query query file name (usually it's a small piece of large subject file(s))
-s/--subject subject file name(s) (comma separated)
-ht/--hashtable single/double single hash table or double hash table method
single hash table method is default setting
single : please set up the key length -k
-k single hash table key length (default:39)
double : please set up the left key length -lk and right key length -rk
-lk double hash table left key length (default:19)
-rk double hash table right key length (default:20)
-or/--orient orientation for the paired end reads in query file(required in MergePairedEndReads)
0-reverse,reverse; 1-reverse,forward; 2-forward,reverse (usually for Illumina reads); 3-forward,forward
-l minimum overlap length (default:40, no need in MergePairedEndReads)
-ll minimum overlap length (default:20, only needed in MergePairedEndReads)
-rl minimum overlap length (default:20, only needed in MergePairedEndReads)
-ol minimum overlap length (default:40, only needed in MergePairedEndReads)
-m maximum allowed mismatch (default:1)
-mr maximum allowed mismatch rate in percentage [1 means 1% of the overlap length]
-t number of threads (default:1 [single thread])
-z stream chunk size of subject read file (default:400)
-o/--out output file name (default:out.txt)
[OPTION]
-h/--help only print out the help contents
Example1: ./storm -i MergePairedEndReads -ht single --query qreads.fasta --orient 2 --subject sreads1.fasta,sreads2.fasta --out outreads -m 0 -ll 30 -rl 30 -ol 60 -k 29 -t 4
Example2: ./storm -i MergePairedEndReads -ht double --query qreads.fasta --orient 2 --subject sreads1.fasta,sreads2.fasta --out outreads -m 1 -ll 10 -rl 10 -ol 20 -lk 4 -rk 4 -t 4
Example3: ./storm -i MergePairedEndReads -ht single --query qreads.fasta --orient 2 --subject sreads1.fasta,sreads2.fasta --out outreads -m 0 -c 3 -b 0.8 -ll 30 -rl 30 -ol 60 -k 29 -t 4
Example4: ./storm -i MergePairedEndReads -ht double --query qreads.fasta --orient 2 --subject sreads1.fasta,sreads2.fasta --out outreads -m 1 -c 5 -b 0.9 -ll 10 -rl 10 -ol 20 -lk 4 -rk 4 -t 4
Qiuming Yao: yao.ornl@gmail.com
Chongle Pan: panc@ornl.gov