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Bioinformatics. 2016 Apr 1;32(7):1009-15. doi: 10.1093/bioinformatics/btv688. Epub 2015 Nov 20.

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Author information

1
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine.
2
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia.
3
Department of Periodontics, University of Washington, Seattle, WA 98195, USA.
4
Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, Department of Computer Science and Engineering, University of California, San Diego, USA and.

Abstract

MOTIVATION:

Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost.

RESULTS:

We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads.

AVAILABILITY AND IMPLEMENTATION:

hybridSPAdes is implemented in C++‚ÄČas a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades

CONTACT:

d.antipov@spbu.ru

SUPPLEMENTARY INFORMATION:

supplementary data are available at Bioinformatics online.

PMID:
26589280
PMCID:
PMC4907386
DOI:
10.1093/bioinformatics/btv688
[Indexed for MEDLINE]
Free PMC Article

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