ALFA 1.1.1-foss-2019a-Python-3.7.2

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

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

2018b

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