TraRECo: a greedy approach based de novo transcriptome assembler with read error correction using consensus matrix.

ABSTRACT:

Background

The challenges when developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize a de Bruijn graph, with which complexity grows linearly with data size while suffering from errors and repeats. Although one can correct the errors by inspecting the topological structure of the graph, this is not an easy task when there are too many branches. Two research directions are to improve either the graph reliability or the path search precision, and in this study, we focused on the former.

Results

We present TraRECo, a greedy approach to de novo assembly employing error-aware graph construction. In the proposed approach, we built contigs by direct read alignment within a distance margin an

SUBMITTER: Yoon S 

PROVIDER: S-EPMC6123912 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature