ALFA 1.1.1-foss-2019a-Python-3.7.2

ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.

Accessing ALFA 1.1.1-foss-2019a-Python-3.7.2

To load the module for ALFA 1.1.1-foss-2019a-Python-3.7.2 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load ALFA/1.1.1-foss-2019a-Python-3.7.2

BEAR Apps Version

2019a

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

  • ALFA 1.1.1
  • progressbar2 3.47.0
  • python utils-2.3.0

More Information

For more information visit the ALFA website.

Dependencies

This version of ALFA has a direct dependency on: foss/2019a matplotlib/3.0.3-foss-2019a-Python-3.7.2 pybedtools/0.8.0-foss-2019a Pysam/0.15.2-foss-2019a Python/3.7.2-GCCcore-8.2.0 SciPy-bundle/2019.03-foss-2019a

Last modified on 11th October 2019