Subread

Description

The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.

Home Page

http://bioinf.wehi.edu.au/subread-package/

Documentation

http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

License

subread is free to use under GNU General Public License version 3.0 (GPLv3).

Usage

Use

module avail subread

to see which versions of subread are available. Use

module load subread/version

Build an index for the reference genome (you may provide a single FASTA file including all the reference sequences):

subread-buildindex -o my_index chr1.fa chr2.fa ...

Map single-end reads using 5 threads:

subread-align -T 5 -i my_index -r reads.txt -o subread_results.sam

Detect indels of up to 16bp:

subread-align -I 16 -i my_index -r reads.txt -o subread_results.sam

Report up to three best mapping locations:

subread-align -B 3 -i my_index -r reads.txt -o subread_results.sam

Report uniquely mapped reads only:

subread-align -u -i my_index -r reads.txt -o subread_results.sam

Map paired-end reads:

subread-align -d 50 -D 600 -i my_index -r reads1.txt -R reads2.txt -o subread_results_PE.sam

subread-align --reportFusions -d 50 -D 600 -i my_index -r reads1.txt -R reads2.txt -o subread_results.sam