Started to work on a cookbook
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## Table of Contents
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- [Installation](#install)
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- [Mapping Genomic Reads](#map-reads)
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## <a name="install"></a>Installation
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```sh
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curl -L https://github.com/lh3/minimap2/releases/download/v2.9/minimap2-2.9_x64-linux.tar.bz2 | tar jxf -
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export PATH="$PATH:"`pwd` # set up PATH
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cp minimap2-2.9_x64-linux/{minimap2,k8,paftools.js} . # copy executables
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cp minimap2-2.9_x64-linux/test/MT-*.fa . # copy small examples
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curl -L https://github.com/lh3/minimap2/releases/download/v2.0/ecoli.tgz | tar zxf -
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```
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## <a name="map-reads"></a>Mapping Genomic Reads
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* Map example E. coli reads (takes about 12 wall-clock seconds):
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```sh
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minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam
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```
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