minimap2 2.24-GCCcore-11.2.0

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.

Accessing minimap2 2.24-GCCcore-11.2.0

To load the module for minimap2 2.24-GCCcore-11.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load minimap2/2.24-GCCcore-11.2.0

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the minimap2 website.

Dependencies

This version of minimap2 has a direct dependency on: GCCcore/11.2.0

Required By

This version of minimap2 is a direct dependent of: CIRI-long/1.1.0-foss-2021b ecc_finder/1.0.0_20221007_67d06f3-foss-2021b nanopolish/0.14.0-foss-2021b

Other Versions

These versions of minimap2 are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 26th July 2022