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

• https://github.com/fmaguire/Bridger_Assembler

Modules | Main Page | Further Topics