Difference between revisions of "Applications/Bridger"
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==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, | + | 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. |
| − | 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. | + | |
| + | Then, 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=== | ||
Revision as of 08:22, 25 April 2017
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
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, 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
[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
Further Information
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