IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels.

ABSTRACT:

Motivation

RNA sequencing based on next-generation sequencing technology is effective for analyzing transcriptomes. Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult. In particular, isoforms can have very uneven expression levels (e.g. 1:100), which make it very difficult to identify low-expressed isoforms. One challenge is to remove erroneous vertices/edges with high multiplicity (produced by high-expressed isoforms) in the de Bruijn graph without removing correct ones with not-so-high multiplicity from low-expressed isoforms. Failing to do so will result in the loss of low-expressed isoforms or having complicated subgraphs with transcripts of different genes mixed together

SUBMITTER: Peng Y 

PROVIDER: S-EPMC3694675 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature