Difference between revisions of "IDBA-UD"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR
* HPC_{{#uppercase:{{#var:app}}}}_BIN
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* HPC_{{uc:{{#var:app}}}}_BIN
 
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{{#if: {{#var: conf}}|==Configuration==
 
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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