Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies.

ABSTRACT:

Background

De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved.

Results

We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to i

SUBMITTER: Cabau C 

PROVIDER: S-EPMC5316280 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature