Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.

ABSTRACT:

Background

The quantity of transcriptome data is rapidly increasing for non-model organisms. As sequencing technology advances, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. Recent studies have compared the performance of different software to establish a best practice for transcriptome assembly. Here, we adapted a simulation approach to evaluate specific features of assembly programs on 454 data. The novelty of our study is that the simulation allows us to calculate a model assembly as reference point for comparison.

Findings

The simulation approach allows us to compare basic metrics of assemblies computed by different software applications (CAP3, MIRA, Newbler, and Oases) to a known optimal solution. We found MIRA

SUBMITTER: Mundry M 

PROVIDER: S-EPMC3288049 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature