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Open Access Technical Note

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

Tongwu Zhang12, Yingfeng Luo1, Yaping Chen1, Xiaonuan Li12 and Jun Yu2*

Author Affiliations

1 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

2 James D. Watson Institute of Genome Sciences, College of life Science, Zhejiang University, Hangzhou 310058, China

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BMC Research Notes 2012, 5:567  doi:10.1186/1756-0500-5-567

Published: 15 October 2012

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 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.