Format

Send to

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

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

Author information

1
Medical Population Genetics, Broad Institute, Cambridge, MA 02142, USA.

Abstract

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:

https://github.com/lh3/minimap and https://github.com/lh3/miniasm

CONTACT:

hengli@broadinstitute.org

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27153593
PMCID:
PMC4937194
DOI:
10.1093/bioinformatics/btw152
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center