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+## Getting Started
+```sh
+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][paf] or
+the [SAM format][sam]. On limited test data sets, minimap2 is over 20 times
+faster than most other long-read aligners.
+
+Minimap2 is the successor of [minimap][minimap]. It uses a similar
+minimizer-based indexing and seeding algorithm, and improves the original
+minimap with homopolyer-compressed k-mers (see also [SMARTdenovo][smartdenovo]
+and [longISLND][longislnd]), better chaining and fast extension alignment (see
+also [libgaba][gaba] and [ksw2][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.
+
+[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
+[sam]: https://samtools.github.io/hts-specs/SAMv1.pdf
+[minimap]: https://github.com/lh3/minimap
+[smartdenovo]: https://github.com/ruanjue/smartdenovo
+[longislnd]: https://www.ncbi.nlm.nih.gov/pubmed/27667791
+[gaba]: https://github.com/ocxtal/libgaba
+[ksw2]: https://github.com/lh3/ksw2