Discover nanopore sequencing

What can it do? How does it work? Our platform performance and accuracy

Explore products

Prepare Sequence Analyse
Store Resources Support About

Minimap2: pairwise alignment for nucleotide sequences


Date: 10th May 2018 | Source:

Authors: Heng Li

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

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.


Bioinformatics - Full text

Recommended for you