70 lines
2.9 KiB
Markdown
70 lines
2.9 KiB
Markdown
## Getting Started
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```sh
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git clone https://github.com/lh3/minimap2
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cd minimap2 && make
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# long reads against a reference genome
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./minimap2 -ax map10k test/MT-human.fa test/MT-orang.fa > test.sam
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# create an index first and then map
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./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa
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./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam
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# long-read overlap (no test data)
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./minimap2 -x ava-pb your-reads.fa your-reads.fa > overlaps.paf
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# man page
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man ./minimap2.1
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```
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## Introduction
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Minimap2 is a fast sequence mapping and alignment program that can find
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overlaps between long noisy reads, or map long reads or their assemblies to a
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reference genome optionally with detailed alignment (i.e. CIGAR). At present,
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it works efficiently with query sequences from a few kilobases to ~100
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megabases in length at an error rate ~15%. Minimap2 outputs in the [PAF][paf] or
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the [SAM format][sam]. On limited test data sets, minimap2 is over 20 times
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faster than most other long-read aligners. It will replace BWA-MEM for long
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reads and contig alignment.
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Minimap2 is the successor of [minimap][minimap]. It uses a similar
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minimizer-based indexing and seeding algorithm, and improves the original
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minimap with homopolyer-compressed k-mers (see also [SMARTdenovo][smartdenovo]
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and [longISLND][longislnd]), better chaining and the ability to produce CIGAR
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with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]) and
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piece-wise affine gap cost.
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## Installation
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For modern x86-64 CPUs, just type `make` in the source code directory. This
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will compile a binary `minimap2` which you can copy to your desired location.
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If you see compilation errors, try `make sse2only=1` to disable SSE4. Minimap2
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will run a little slower. At present, minimap2 does not work with non-x86 CPUs
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or ancient CPUs that do not support SSE2. SSE2 is critical to the performance
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of minimap2.
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## Limitations
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* At the alignment phase, minimap2 performs global alignments between minimizer
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hits. If the positions of these minimizer hits are incorrect, the final
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alignment may be suboptimal or unnecessarily fragmented.
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* Minimap2 may produce poor alignments that may need post-filtering. We are
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still exploring a reliable and consistent way to report good alignments.
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* Minimap2 does not work well with Illumina short reads as of now.
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* Minimap2 requires SSE2 instructions to compile. It is possible to add
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non-SSE2 support, but it would make minimap2 slower by several times.
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In general, minimap2 is a young project with most code written since June,
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2017. It may have bugs and room for improvements. Bug reports and suggestions
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are warmly welcomed.
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[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
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[sam]: https://samtools.github.io/hts-specs/SAMv1.pdf
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[minimap]: https://github.com/lh3/minimap
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[smartdenovo]: https://github.com/ruanjue/smartdenovo
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[longislnd]: https://www.ncbi.nlm.nih.gov/pubmed/27667791
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[gaba]: https://github.com/ocxtal/libgaba
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[ksw2]: https://github.com/lh3/ksw2
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