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

Bioinformatics. 2016 Apr 1;32(7):1009-15. doi: 10.1093/bioinformatics/btv688. Epub 2015 Nov 20.


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.

MeSH terms

  • Algorithms*
  • Base Sequence
  • Chromosome Mapping
  • Genome
  • Sequence Analysis, DNA*