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Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266.

ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Author information

1
Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.
2
Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USAAlgorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia, Department of Mathematics and Mechanics, Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia and Department of Computer Science and Engineering, University of California, San Diego, USA.

Abstract

Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

AVAILABILITY AND IMPLEMENTATION:

http://bioinf.spbau.ru/en/spades

PMID:
24931996
PMCID:
PMC4058921
DOI:
10.1093/bioinformatics/btu266
[Indexed for MEDLINE]
Free PMC Article

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