Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing.

ABSTRACT: DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the "good" transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly prog

SUBMITTER: Misner I 

PROVIDER: S-EPMC3708500 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature