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Bioinformatics. 2015 Oct 15;31(20):3262-8. doi: 10.1093/bioinformatics/btv337. Epub 2015 Jun 3.

Assembling short reads from jumping libraries with large insert sizes.

Author information

1
Algorithmic Biology Lab, St. Petersburg Academic University 194021.
2
Algorithmic Biology Lab, St. Petersburg Academic University 194021, Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004.
3
Algorithmic Biology Lab, St. Petersburg Academic University 194021, Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004, Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, 198504, Russia and.
4
Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004, Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0404, USA.

Abstract

MOTIVATION:

Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies.

RESULTS:

We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads.

AVAILABILITY AND IMPLEMENTATION:

Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades.

CONTACT:

ap@bioinf.spbau.ru

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26040456
DOI:
10.1093/bioinformatics/btv337
[Indexed for MEDLINE]

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