Minimap2: pairwise alignment for nucleotide sequences

TL;DR

Minimap2 is a versatile, fast, and accurate alignment tool designed for mapping various types of long and short nucleotide sequences against large reference genomes, outperforming existing aligners in speed and accuracy.

Contribution

It introduces a new alignment algorithm capable of handling ultra-long reads, noisy data, and large genomes efficiently, with novel heuristics to improve accuracy and reduce spurious matches.

Findings

3-4 times faster than mainstream short-read mappers

Over 30 times faster at higher accuracy for long reads

Effective for diverse sequencing data types

Abstract

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (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 $\ge$100bp in length, $\ge$1kb genomic reads at error rate $\sim$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 (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times faster than mainstream short-read mappers at comparable accuracy and $\ge$30 times faster at higher accuracy for both genomic and mRNA reads, surpassing most aligners specialized in one type of alignment. Availability and implementation: https://github.com/lh3/minimap2 Contact: hengli@broadinstitute.org