Journal
BIOINFORMATICS
Volume 30, Issue 12, Pages 293-301Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu266
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Funding
- Government of the Russian Federation [11. G34.31.0018, 11. G34.31.0068]
- National Institutes of Health [3P41RR024851-02S1]
- Russian Fund for Basic Research [12-01-00747-a]
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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.
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