BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler.

ABSTRACT:

Background

As more and more reference genome sequences are assembled, it becomes practical to assemble individual genomes from large amount of raw read data based on a reference sequence. However, most available assembly tools are designed for de-novo genome assembly. There is one commercial tool box (Newbler) developed for re-sequencing projects based on the Roche 454 sequencing platform. However, the genome with large repeat regions cannot be well assembled in Newbler.

Findings

We developed a new sequence assembly tool (BIGrat, Beijing Institute of Genomics Re-Assembly Tool) for pyrosequencing-based re-sequencing projects, such as data generated from Roche 454 and IonTorrent platforms. BIGrat improves the output of Newbler when evaluated on genome assemblies including chlo

SUBMITTER: Zhang T 

PROVIDER: S-EPMC3599625 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature