Snippy¶

Snippy finds both substitutions (SNPs) and insertions/deletions (indels) between a haploid reference genome and your NGS sequence reads. The bundle packages version 4.6.0.

Usage example¶

The following command can be executed in the terminal to load the bundle:

1	`module load snippy`

The Snippy commands can be run as shown below:

snippy
snippy-clean_full_aln
snippy-core
snippy-multi
snippy-vcf_extract_subs
snippy-vcf_report
snippy-vcf_to_tab

The snippy_shell command can be used to access a shell in the bundle.

1	`snippy_shell`

Performance notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

Snippy is licensed under the GNU GPLv2 license.

Primary citation¶

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za