SortMeRNA 4.3.6-foss-2021b

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

Accessing SortMeRNA 4.3.6-foss-2021b

To load the module for SortMeRNA 4.3.6-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load SortMeRNA/4.3.6-foss-2021b

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake

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 SortMeRNA website.

Dependencies

This version of SortMeRNA has a direct dependency on: ConcurrentQueue/1.0.3-GCCcore-11.2.0 foss/2021b RapidJSON/1.1.0-GCCcore-11.2.0 RocksDB/7.9.2-GCCcore-11.2.0 zlib/1.2.11-GCCcore-11.2.0

Last modified on 16th February 2023