segemehl 0.3.4-GCC-9.3.0

segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

Accessing segemehl 0.3.4-GCC-9.3.0

To load the module for segemehl 0.3.4-GCC-9.3.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load segemehl/0.3.4-GCC-9.3.0

BEAR Apps Version

2020a

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.

More Information

For more information visit the segemehl website.

Dependencies

This version of segemehl has a direct dependency on: GCC/9.3.0 HTSlib/1.10.2-GCC-9.3.0 ncurses/6.2-GCCcore-9.3.0 zlib/1.2.11-GCCcore-9.3.0

Last modified on 27th May 2021