snippy 4.6.0-foss-2019b-Perl-5.30.0

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

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, BEAR Cloud VMs, and CaStLeS VMs):

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

BEAR Apps Version


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.


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