PASApipeline 2.4.1-foss-2019b

PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Accessing PASApipeline 2.4.1-foss-2019b

To load the module for PASApipeline 2.4.1-foss-2019b please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load PASApipeline/2.4.1-foss-2019b

BEAR Apps Version

2019b

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 Cloud and CaStLeS 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 PASApipeline website.

Dependencies

This version of PASApipeline has a direct dependency on: FASTA/36.3.8h_04-May-2020-foss-2019b foss/2019b GMAP-GSNAP/2020-09-12-foss-2019b Kent_tools/401-foss-2019b Perl/5.30.0-GCCcore-8.3.0 SQLite/3.29.0-GCCcore-8.3.0

Required By

This version of PASApipeline is a direct dependent of: funannotate/1.8.1-foss-2019b-Python-2.7.16 funannotate/1.8.1-foss-2019b-Python-3.7.4

Last modified on 12th October 2020