Difference between revisions of "Bridger"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGSCategory:Assembler {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|bridger}} |{{#vardefine:url|https://s...") |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 13:14, 15 August 2022
Description
Bridger is an efficient de novo transcriptome assembler for RNA-Seq data. It expects as input RNA-Seq reads (single or paired) in fasta or fastq format, outputs all transcripts in fasta format, without using a reference genome. Briefly, it works in two steps: 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, for each splicing graph, Bridger uses a rigorous mathematical model called minimum path cover to search an optimal set of paths (transcripts) that can be supported by sequence data and could explain all observed splicing events of each locus.
Environment Modules
Run module spider bridger to find out what environment modules are available for this application.
System Variables
- HPC_BRIDGER_DIR - installation directory