Minimap2 2016

Introduction

Note: minimap2 has replaced BWA-MEM for PacBio and Nanopore read alignment. It retains all major BWA-MEM features, but is ~50 times as fast, more versatile, more accurate and produces better base-level alignment. ¹
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full-genome alignment between two closely related species with divergence below ~15%. ¹

Installed version(s)

This version is installed and currently available on environment hpc-env/6.4:

• minimap2/2.13-foss-2017b

... and on enviropnment hpc-env/8.3:

• minimap2/2.22-GCCcore-8.3.0

Using minimap2

If you want to find out more about minimap2 on the HPC cluster, you can use the command

module spider minimap2

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env 6.4
module load minimap2

Always remember: this command is case sensitive!

If you need more information on how to use minimap2 (arguments, options, etc), just type in the main function after loading the module:

minimap2

Documentation

The project page as well as te full documentation can be found here.