BWA-Teaching: Difference between revisions
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=== Version === | === Version === | ||
0.7. | 0.7.17 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/eb/BWA/0.7. | The last version of this application is at /usr/local/apps/eb/BWA/0.7.17-foss-2016b | ||
To use this version, please loads the module with | To use this version, please loads the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml BWA/0.7. | ml BWA/0.7.17-foss-2016b | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml BWA/0.7.17-foss-2016b<br> | |||
ml | bwa <u>[options]</u><br> | ||
</div> | </div> | ||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values | 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]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster. | Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster. | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
BWA/0.7. | ml BWA/0.7.17-foss-2016b | ||
bwa | bwa bwa | ||
Program: bwa (alignment via Burrows-Wheeler transformation) | Program: bwa (alignment via Burrows-Wheeler transformation) | ||
Version: 0.7. | Version: 0.7.17-r1188 | ||
Contact: Heng Li <lh3@sanger.ac.uk> | Contact: Heng Li <lh3@sanger.ac.uk> | ||
Revision as of 10:37, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
0.7.17
Author / Distributor
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
The last version of this application is at /usr/local/apps/eb/BWA/0.7.17-foss-2016b
To use this version, please loads the module with
ml BWA/0.7.17-foss-2016b
Here is an example of a shell script, sub.sh, to run on at 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
cd $SLURM_SUBMIT_DIR
ml BWA/0.7.17-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/0.7.17-foss-2016b
bwa bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
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.
Installation
Source code is obtained from BWA
System
64-bit Linux