BWA-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.7.15, 0.7.17

Author / Distributor

BWA

Description

"Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome." More details are at BWA

Running Program

Version 0.7.15

Installed in /usr/local/apps/eb/BWA/0.7.15-foss-2016b

To use this version, please load the module with

ml BWA/0.7.15-foss-2016b 

Version 0.7.17

Installed in /usr/local/apps/eb/BWA/0.7.17-foss-2016b

To use this version, please load the module with

ml BWA/0.7.17-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_BWA
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BWA.%j.out
#SBATCH --error=BWA.%j.err

cd $SLURM_SUBMIT_DIR
ml BWA/0.7.15-foss-2016b
bwa [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml BWA/0.7.15-foss-2016b 
bwa 

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.15-r1140
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

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Installation

Source code is obtained from BWA

System

64-bit Linux