A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

ABSTRACT: The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM) occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer read

SUBMITTER: Zhang W 

PROVIDER: S-EPMC3056720 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature