Assembling short reads from jumping libraries with large insert sizes.

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.

ExSPAnder: a universal repeat resolver for DNA fragment assembly.

UNLABELLED: 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