HPC

Difference between revisions of "Applications/Bridger"

From HPC
Jump to: navigation , search
(Created page with "__TOC__ ==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...")
 
m (→‎Batch Job)
 
(9 intermediate revisions by the same user not shown)
Line 4: Line 4:
 
*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
−
*Licence: GNU
+
*Licence: [https://github.com/fmaguire/Bridger_Assembler Github], open source
  
 
==Usage Examples==
 
==Usage Examples==
  
−
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,
+
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.
−
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.
+
 
  
 
===Module===
 
===Module===
Line 27: Line 27:
 
</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==
  
−
* [http://www.boost.org/ http://www.boost.org/]
+
* [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler]
  
−
{|
+
{{Modulepagenav}}
−
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
−
|style="width:95%; border-width: 0" |
 
−
* [[Main_Page|Home]]
 
−
* [[Applications|Application support]]
 
−
* [[General|General]]
 
−
* [[Training|Training]]
 
−
* [[Programming|Programming support]]
 
−
|-
 
−
|}
 

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

Retrieved from ‘http://hpc.mediawiki.hull.ac.uk/index.php?title=Applications/Bridger&oldid=41180’