Minimap2 是一个快速序列映射和校准程序

Minimap2 是一个快速序列映射和校准程序

Getting Started

git clone https://github.com/lh3/minimap2cd 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 pageman ./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.

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