From f78a2477495891e848a9878418f9e94af3089020 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 12 Mar 2018 12:00:44 -0400
Subject: [PATCH] Started to work on a cookbook

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 cookbook.md | 21 +++++++++++++++++++++
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+## Table of Contents
+
+- [Installation](#install)
+- [Mapping Genomic Reads](#map-reads)
+
+## <a name="install"></a>Installation
+
+```sh
+curl -L https://github.com/lh3/minimap2/releases/download/v2.9/minimap2-2.9_x64-linux.tar.bz2 | tar jxf -
+export PATH="$PATH:"`pwd`                              # set up PATH
+cp minimap2-2.9_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+cp minimap2-2.9_x64-linux/test/MT-*.fa .               # copy small examples
+curl -L https://github.com/lh3/minimap2/releases/download/v2.0/ecoli.tgz | tar zxf -
+```
+
+## <a name="map-reads"></a>Mapping Genomic Reads
+
+* Map example E. coli reads (takes about 12 wall-clock seconds):
+  ```sh
+  minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam
+  ```