snippy
rapid haploid variant calling and core genome alignment
Command lineScience
Not tested on a device yet. What that means
Commands in the package
snippysnippy-clean_full_alnsnippy-coresnippy-multisnippy-vcf_extract_subssnippy-vcf_reportsnippy-vcf_to_tab
About snippy
From Debian's package description
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).
From Debian's description of the snippy package, under that package's license.
Dependencies
Depends on
Related apps
- vcftoolsCollection of tools to work with VCF filesCommand line
- bioperlPerl tools for computational molecular biologyCommand line
- primer3tool to design flanking oligo nucleotides for DNA amplificationCommand line
- hhsuitesensitive protein sequence searching based on HMM-HMM alignmentCommand line
- staden-io-lib-utilsprograms for manipulating DNA sequencing filesCommand line
- sim4dbbatch spliced alignment of cDNA sequences to a target genomeCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the snippy package, under that package's license.
- Description: Debian's description of the snippy package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.