Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19.


Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads.

Results: We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools.

Availability and implementation: and


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Animals
  • Bacteria / genetics
  • Caenorhabditis elegans / genetics
  • Chromosome Mapping / methods*
  • Computational Biology
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Sequence Analysis, DNA
  • Software*