snippy 4.6.0-foss-2019b-Perl-5.30.0

Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment.

Accessing snippy 4.6.0-foss-2019b-Perl-5.30.0

To load the module for snippy 4.6.0-foss-2019b-Perl-5.30.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load snippy/4.6.0-foss-2019b-Perl-5.30.0

BEAR Apps Version

2019b

Architectures

EL8-cascadelakeEL8-haswellUbuntu20.04-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.

snippy and Python

Some snippy functions require Python. If you get an error message /usr/bin/env: 'python': No such file or directory then you should also load Python with module load Python/3.7.4-GCCcore-8.3.0.

More Information

For more information visit the snippy website.

Dependencies

This version of snippy has a direct dependency on: BCFtools/1.10.2-GCC-8.3.0 BioPerl/1.7.2-GCCcore-8.3.0 foss/2019b Java/11 Perl/5.30.0-GCCcore-8.3.0 SAMtools/1.10-GCC-8.3.0 seqtk/1.3-GCC-8.3.0 vt/2187ff6-foss-2019b

Last modified on 10th November 2020