Difference between revisions of "IDBA-UD"

From UFRC
Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BioinformaticsCategory:Metagenomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|idba}} |{{#vardefine:url|http://i.cs.hku.hk/~alse/...")
 
m (Text replacement - "#uppercase" to "uc")
 
(One intermediate revision by one other user not shown)
Line 33: Line 33:
 
-->
 
-->
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
+
* HPC_{{uc:{{#var:app}}}}_DIR
* HPC_{{#uppercase:{{#var:app}}}}_BIN
+
* HPC_{{uc:{{#var:app}}}}_BIN
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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

Latest revision as of 21:21, 6 December 2019

Description

idba website  

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_IDBA_DIR
  • HPC_IDBA_BIN





Validation

  • Validated 4/5/2018