TY - GEN

T1 - Assembling genomes and mini-metagenomes from highly chimeric reads

AU - Nurk, Sergey

AU - Bankevich, Anton

AU - Antipov, Dmitry

AU - Gurevich, Alexey

AU - Korobeynikov, Anton

AU - Lapidus, Alla

AU - Prjibelsky, Andrey

AU - Pyshkin, Alexey

AU - Sirotkin, Alexander

AU - Sirotkin, Yakov

AU - Stepanauskas, Ramunas

AU - McLean, Jeffrey

AU - Lasken, Roger

AU - Clingenpeel, Scott R.

AU - Woyke, Tanja

AU - Tesler, Glenn

AU - Alekseyev, Max A.

AU - Pevzner, Pavel A.

PY - 2013

Y1 - 2013

N2 - Recent advances in single-cell genomics provide an alternative to gene-centric metagenomics studies, enabling whole genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly non-uniform read coverage, and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "dark matter of life" that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. We demonstrate that SPAdes enables sequencing mini-metagenomes and benchmark it against various assemblers. On single-cell bacterial datasets, SPAdes improves on the recently developed E+V-SC and IDBA-UD assemblers specifically designed for single-cell sequencing. For standard (multicell) datasets, SPAdes also improves on A5, ABySS, CLC, EULER-SR, Ray, SOAPdenovo, and Velvet.

AB - Recent advances in single-cell genomics provide an alternative to gene-centric metagenomics studies, enabling whole genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly non-uniform read coverage, and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "dark matter of life" that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. We demonstrate that SPAdes enables sequencing mini-metagenomes and benchmark it against various assemblers. On single-cell bacterial datasets, SPAdes improves on the recently developed E+V-SC and IDBA-UD assemblers specifically designed for single-cell sequencing. For standard (multicell) datasets, SPAdes also improves on A5, ABySS, CLC, EULER-SR, Ray, SOAPdenovo, and Velvet.

UR - http://www.scopus.com/inward/record.url?scp=84875487500&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-37195-0_13

DO - 10.1007/978-3-642-37195-0_13

M3 - Conference contribution

AN - SCOPUS:84875487500

SN - 9783642371943

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 158

EP - 170

BT - Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings

T2 - 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013

Y2 - 7 April 2013 through 10 April 2013

ER -