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

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 chloroplast, mitochondrial, bacterial, and plant nuclear genomes. CONCLUSION: We presented a novel sequence assembly tool BIGrat for pyrosequencing-based re-sequencing projects, which can easily be integrated into Newbler pipelines for next-generation sequencing assembly and analysis.