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Difference between revisions of "Applications/Bridger"

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*Version: r2014-12-01, r2014-12-01.1 and r2014-12-01.2
 
*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
 
*Module: bridger/r2014-12-01, bridger/r2014-12-01.1, and bridger/r2014-12-01.2
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*Licence: GNU
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*Licence: [https://github.com/fmaguire/Bridger_Assembler Github], open source
  
 
==Usage Examples==
 
==Usage Examples==
  
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Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.  The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Briefly, it works in two step: first,  Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes. Then,
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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.
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Bridger uses a rigorous mathematical model called minimum path cover to search minimal set of paths(transcripts) that can be supported by our data and could explain all observed splicing events of each locus.
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===Module===
 
===Module===
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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==
  
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* [http://www.boost.org/ http://www.boost.org/]
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* [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler]
  
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{|
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{{Modulepagenav}}
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|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
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|style="width:95%; border-width: 0" |
 
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* [[Main_Page|Home]]
 
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* [[Applications|Application support]]
 
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* [[General|General]]
 
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* [[Training|Training]]
 
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* [[Programming|Programming support]]
 
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|-
 
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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

Further Information





Modules | Main Page | Further Topics

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