Dataset Information

HybridSPAdes: an algorithm for hybrid assembly of short and long reads.

ABSTRACT:

Motivation

Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost.

Results

We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads.

Availability and implementation

hybridSPAdes is implemented in C++ as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades

Contact

d.antipov@spbu.ru

Supplementary information

supplementary data are available at Bioinformatics online.

SUBMITTER: Antipov D

PROVIDER: S-EPMC4907386 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Antipov Dmitry D Korobeynikov Anton A McLean Jeffrey S JS Pevzner Pavel A PA

Bioinformatics (Oxford, England) 20151120 7

<h4>Motivation</h4>Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assembli ...[more]

PMID: 26589280

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