Getting Started

git clone https://github.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 ava-pb 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 an 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. It will replace BWA-MEM for long reads and contig alignment.

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) and piece-wise affine gap cost.

Installation

For modern x86-64 CPUs, just type make in the source code directory. This will compile a binary minimap2 which you can copy to your desired location. If you see compilation errors, try make sse2only=1 to disable SSE4. Minimap2 will run a little slower. At present, minimap2 does not work with non-x86 CPUs or ancient CPUs that do not support SSE2. SSE2 is critical to the performance of minimap2.

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 unnecessarily fragmented.

• Minimap2 may produce poor alignments that may need post-filtering. We are still exploring a reliable and consistent way to report good alignments.

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

• Minimap2 requires SSE2 instructions to compile. It is possible to add non-SSE2 support, but it would make minimap2 slower by several times.

In general, minimap2 is a young project with most code written since June, 2017. It may have bugs and room for improvements. Bug reports and suggestions are warmly welcomed.