Difference between revisions of "Bridger"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGSCategory:Assembler {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|bridger}} |{{#vardefine:url|https://s...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
(One intermediate revision by one other user not shown) | |||
Line 34: | Line 34: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Line 76: | Line 76: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
+ | =Validation= | ||
+ | * Validate 4/5/2018 |
Revision as of 21:11, 6 December 2019
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.
Required Modules
Serial
- bridger
System Variables
- HPC_BRIDGER_DIR - installation directory
Validation
- Validate 4/5/2018