A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

ABSTRACT: Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC4133164 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature