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PLoS One. 2014 Sep 8;9(9):e107014. doi: 10.1371/journal.pone.0107014. eCollection 2014.

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.

Author information

1
Department for Periodontology, University of Münster, Münster, Germany; Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
2
Department for Periodontology, University of Münster, Münster, Germany.
3
Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
4
Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
5
Bioinformatics and Systems Biology, Justus-Liebig-Univeristy Gießen, Gießen, Germany.
6
Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany; Genome Informatics Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany.

Abstract

De novo genome assembly is the process of reconstructing a complete genomic sequence from countless small sequencing reads. Due to the complexity of this task, numerous genome assemblers have been developed to cope with different requirements and the different kinds of data provided by sequencers within the fast evolving field of next-generation sequencing technologies. In particular, the recently introduced generation of benchtop sequencers, like Illumina's MiSeq and Ion Torrent's Personal Genome Machine (PGM), popularized the easy, fast, and cheap sequencing of bacterial organisms to a broad range of academic and clinical institutions. With a strong pragmatic focus, here, we give a novel insight into the line of assembly evaluation surveys as we benchmark popular de novo genome assemblers based on bacterial data generated by benchtop sequencers. Therefore, single-library assemblies were generated, assembled, and compared to each other by metrics describing assembly contiguity and accuracy, and also by practice-oriented criteria as for instance computing time. In addition, we extensively analyzed the effect of the depth of coverage on the genome assemblies within reasonable ranges and the k-mer optimization problem of de Bruijn Graph assemblers. Our results show that, although both MiSeq and PGM allow for good genome assemblies, they require different approaches. They not only pair with different assembler types, but also affect assemblies differently regarding the depth of coverage where oversampling can become problematic. Assemblies vary greatly with respect to contiguity and accuracy but also by the requirement on the computing power. Consequently, no assembler can be rated best for all preconditions. Instead, the given kind of data, the demands on assembly quality, and the available computing infrastructure determines which assembler suits best. The data sets, scripts and all additional information needed to replicate our results are freely available at ftp://ftp.cebitec.uni-bielefeld.de/pub/GABenchToB.

PMID:
25198770
PMCID:
PMC4157817
DOI:
10.1371/journal.pone.0107014
[Indexed for MEDLINE]
Free PMC Article

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