amplimap 0.4.16-foss-2018b-Python-3.6.6

Deprecated: Use of this version of amplimap is deprecated. More information on our Applications Support and Retention Policy.

amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing (NGS) experiments with PCR-based amplicons or capture-based enrichment systems.

Accessing amplimap 0.4.16-foss-2018b-Python-3.6.6

To load the module for amplimap 0.4.16-foss-2018b-Python-3.6.6 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load amplimap/0.4.16-foss-2018b-Python-3.6.6

BEAR Apps Version

2018b

Architectures

EL8-cascadelake — EL8-haswell — 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.

Extensions

  • amplimap 0.4.16
  • Distance 0.1.3
  • future 0.17.1
  • interlap 0.2.6
  • pyfaidx 0.5.5.2
  • pysam 0.13
  • regex 2019.01.24
  • umi_tools 0.5.5

More Information

For more information visit the amplimap website.

Dependencies

This version of amplimap has a direct dependency on: Biopython/1.72-foss-2018b-Python-3.6.6 cURL/7.60.0-GCCcore-7.3.0 foss/2018b matplotlib/3.0.0-foss-2018b-Python-3.6.6 ncurses/6.1-GCCcore-7.3.0 Python/3.6.6-foss-2018b PyYAML/3.13-foss-2018b-Python-3.6.6 snakemake/5.2.4-foss-2018b-Python-3.6.6

Other Versions

These versions of amplimap 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.

Version BEAR Apps Version
0.4.5-foss-2018b-Python-3.6.6 2018b

Last modified on 19th February 2021