minimap2
Minimap2 is a fast sequence mapping and alignmentprogram that can find overlaps between long noisy reads, or map longreads or their assemblies to a reference genome optionally with detailedalignment (i.e. CIGAR). At present, it works efficiently with querysequences from a few kilobases to ~100 megabases in length at an errorrate ~15%. Minimap2 outputs in the PAF or the SAM format. On limitedtest data sets, minimap2 is over 20 times faster than most otherlong-read aligners. It will replace BWA-MEM for long reads and contigalignment.
https://github.com/lh3/minimap2
Available modules
The overview below shows which minimap2 installations are available per target architecture in the HPCC module system, ordered based on software version (new to old).
To start using minimap2, load one of these modules using a module load command like:
1 | |
(This data was automatically generated on Thu, 17 Apr 2025 at 12:00:12 EDT)
| neoverse_v1 | generic | zen2 | zen3 | zen4 | haswell | skylake_avx512 | |
|---|---|---|---|---|---|---|---|
| Grace Nodes | everywhere (except Grace nodes) | amd20 | amd22 | amd24 | intel16 | intel18,amd20-v100,amd21,intel21 | |
| minimap2/2.26-GCCcore-12.3.0 | - | x | - | - | - | - | - |
| minimap2/2.26-GCCcore-12.2.0 | - | x | - | - | - | - | - |