SRAssembler: Selective Recursive local Assembly of homologous genomic regions.

ABSTRACT:

Background

The falling cost of next-generation sequencing technology has allowed deep sequencing across related species and of individuals within species. Whole genome assemblies from these data remain high time- and resource-consuming computational tasks, particularly if best solutions are sought using different assembly strategies and parameter sets. However, in many cases, the underlying research questions are not genome-wide but rather target specific genes or sets of genes. We describe a novel assembly tool, SRAssembler, that efficiently assembles only contigs containing potential homologs of a gene or protein query, thus enabling gene-specific genome studies over large numbers of short read samples.

Results

We demonstrate the functionality of SRAssembler with examples

SUBMITTER: McCarthy TW 

PROVIDER: S-EPMC6604332 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature