Minimap2: pairwise alignment for nucleotide sequences.

Bioinformatics
Authors
Keywords
Abstract

Motivation: Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

Results: Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment.

Availability and implementation: https://github.com/lh3/minimap2.

Supplementary information: Supplementary data are available at Bioinformatics online.

Year of Publication
2018
Journal
Bioinformatics
Volume
34
Issue
18
Pages
3094-3100
Date Published
2018 09 15
ISSN
1367-4811
DOI
10.1093/bioinformatics/bty191
PubMed ID
29750242
PubMed Central ID
PMC6137996
Links
Grant list
R01 HG010040 / HG / NHGRI NIH HHS / United States