Difference between revisions of "Applications/Bridger"

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</pre>
 
</pre>
  
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===Batch Job===
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<pre>
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#!/bin/bash
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#SBATCH -J bowtie_testing
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#SBATCH -p=compute
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#SBATCH --exclusive
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#SBATCH -o %N.%j.out
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#SBATCH -e %N.%j.err
  
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module purge
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module add boost/gcc/1.61.0
  
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Assemble -h
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Bridger.pl --seqType fq --left reads.left.fq --right reads.right.fq --CPU 6
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</pre>
  
 
==Further Information==
 
==Further Information==

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

Further Information





Modules | Main Page | Further Topics