Difference between revisions of "IDBA-UD"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:Metagenomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|idba}} |{{#vardefine:url|http://i.cs.hku.hk/~alse/...") |
|||
| Line 68: | Line 68: | ||
<!--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= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 17:45, 5 April 2018
Description
IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
Required Modules
Serial
- idba
System Variables
- HPC_{{#uppercase:idba}}_DIR
- HPC_{{#uppercase:idba}}_BIN
Validation
- Validated 4/5/2018