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## Getting Started
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```sh
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git clone https://gitlab.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 ava10k 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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2017-07-17 05:52:57 +08:00
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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.
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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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two-piece affine gap cost.
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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 alignment
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may be suboptimal or broken due to the Z-drop heuristics. In addition, in the
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event of a long insertion/deletion, minimap2 may split the long event into
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a few smaller events. We will address these issues in future.
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Minimap2 does not work well with Illumina short reads as of now.
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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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