Difference between revisions of "Applications/Bridger"
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</pre> | </pre> | ||
| + | ===Batch Job=== | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH -J bowtie_testing | ||
| + | #SBATCH -p=compute | ||
| + | #SBATCH --exclusive | ||
| + | #SBATCH -o %N.%j.out | ||
| + | #SBATCH -e %N.%j.err | ||
| + | module purge | ||
| + | module add boost/gcc/1.61.0 | ||
| + | Assemble -h | ||
| + | Bridger.pl --seqType fq --left reads.left.fq --right reads.right.fq --CPU 6 | ||
| + | </pre> | ||
==Further Information== | ==Further Information== | ||
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* [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler] | * [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler] | ||
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Latest revision as of 10:45, 17 November 2022
Application Details
- Description: Bridger is an efficient de novo trascriptome assembler for RNA-Seq data.
- Version: r2014-12-01, r2014-12-01.1 and r2014-12-01.2
- Module: bridger/r2014-12-01, bridger/r2014-12-01.1, and bridger/r2014-12-01.2
- Licence: Github, open source
Usage Examples
Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing.
Module
[username@login01 ~]$ module add boost/gcc/1.61.0
[username@login01 ~]$ Assemble -h
===============================================================================
Usage: Assemble [--reads/--kmers] <filename> [opts]
===============================================================================
...
[username@login01 ~]$ Bridger.pl --seqType fq --left reads.left.fq --right reads.right.fq --CPU 6
Batch Job
#!/bin/bash #SBATCH -J bowtie_testing #SBATCH -p=compute #SBATCH --exclusive #SBATCH -o %N.%j.out #SBATCH -e %N.%j.err module purge module add boost/gcc/1.61.0 Assemble -h Bridger.pl --seqType fq --left reads.left.fq --right reads.right.fq --CPU 6