minimap2/cookbook.md

Table of Contents

• Installation
• Mapping Genomic Reads

Installation

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 -

Mapping Genomic Reads

• Map example E. coli reads (takes about 12 wall-clock seconds):

  minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam