Comparing de novo assemblers for 454 transcriptome data.

ABSTRACT:

Background

Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis.

Results

Although no single assembler performed best on all our criteria, New

SUBMITTER: Kumar S 

PROVIDER: S-EPMC3091720 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature