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

Bioinformatics
Authors
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.

Year of Publication
2016
Journal
Bioinformatics
Volume
32
Issue
14
Pages
2103-10
Date Published
2016 Jul 15
ISSN
1367-4811
URL
DOI
10.1093/bioinformatics/btw152
PubMed ID
27153593
PubMed Central ID
PMC4937194
Links
Grant list
R01 GM100233 / GM / NIGMS NIH HHS / United States