Difference between revisions of "IDBA-MT"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|idba-mt}} |{{#vardefine:url|http://i.cs.hku.hk/~alse/hkubrg/projec...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (One intermediate revision by the same user not shown) | |||
| Line 22: | Line 22: | ||
IDBA-MTP is an optional pre-processing software for IDBA-MT. It generates candidate contigs by aligning reference protein sequences to de Bruijn graph. Please run IDBA-UD and IDBA-MT after running IDBA-MTP to get confident result. | IDBA-MTP is an optional pre-processing software for IDBA-MT. It generates candidate contigs by aligning reference protein sequences to de Bruijn graph. Please run IDBA-UD and IDBA-MT after running IDBA-MTP to get confident result. | ||
| − | + | ==Environment Modules== | |
| − | == | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
| − | |||
| − | |||
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 21:21, 6 December 2019
Description
IDBA-MT is an iterative De Bruijn Graph De Novo short read assembler for meta-transcriptome. It is purely de novo assembler based on paired-end RNA sequencing reads only. IDBA-MT is a post-processing software for IDBA-UD contigs for removing chimeria contigs and extending contig length using paired-end reads information.
IDBA-MTP is an optional pre-processing software for IDBA-MT. It generates candidate contigs by aligning reference protein sequences to de Bruijn graph. Please run IDBA-UD and IDBA-MT after running IDBA-MTP to get confident result.
Environment Modules
Run module spider idba-mt to find out what environment modules are available for this application.
System Variables
- HPC_IDBA-MT_DIR - installation directory