Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.

ABSTRACT:

Background

RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems, we compare de novo assemblies of paired end 90 bp RNA-seq reads using Oases, Trinity, Trans-ABySS and SOAPdenovo-Trans to transcripts from genome annotation of the model plant Ricinus communis. By doing so we evaluate strategies for optimizing total gene coverage and minimizing assembly chimeras and redundancy.

Results

We found that the frequency and structure of chimeras vary dramatically among different software packages. The differences were largely due to

SUBMITTER: Yang Y 

PROVIDER: S-EPMC3663818 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature