Getting Started

git clone https://gitlab.com/lh3/minimap2
cd minimap2 && make
# long reads against a reference genome
./minimap2 -ax map10k test/MT-human.fa test/MT-orang.fa > test.sam
# create an index first and then map
./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa
./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam
# long-read overlap (no test data)
./minimap2 -x ava10k your-reads.fa your-reads.fa > overlaps.paf
# man page
man ./minimap2.1

Introduction

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners.

Minimap2 is the successor of minimap. It uses a similar minimizer-based indexing and seeding algorithm, and improves the original minimap with homopolyer-compressed k-mers (see also SMARTdenovo and longISLND), better chaining and the ability to produce CIGAR with fast extension alignment (see also libgaba and ksw2).

Limitations

At the alignment phase, minimap2 performs global alignments between minimizer hits. If the positions of these minimizer hits are incorrect, the final alignment may be suboptimal or broken due to the Z-drop heuristics. In addition, in the event of a long insertion/deletion, minimap2 may split the long event into a few smaller events. We will address these issues in future.

Minimap2 does not work well with Illumina short reads as of now.