ExSPAnder

ExSPAnder: a universal repeat resolver for DNA fragment assembly. 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

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  1. Komusiewicz, Christian; Radulescu, Andreea: On the sound covering cycle problem in paired de Bruijn graphs (2015)