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

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.