Snippy specifications

Information


Unique identifier OMICS_03551
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference genome and a sequence read files.
Input format FASTA, GENBANK, FASTQ
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.2
Stability Stable
Requirements bwa mem, samtools, GNU parallel, freebayes, vcflib, vcftools, snpEff
Maintained Yes

Taxon


  • Eubacteria

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Documentation


Maintainer


  • person_outline Torsten Seemann <>

Snippy citation

2017
PMCID: 5635451

[…] id prjna295807. the raw reads were assembled into contigs using spades 3.9.0 (nurk et al., 2013) and mapped to the fully assembled chromosome of s. aureus col (st250) (chromosome: cp000046) using snippy v3.21. mlst and antibiotic resistance detection were undertaken with mlst v2.82 and abricate v0.5-dev3, respectively. maximum likelihood phylogenetic trees were generated using an alignment […]

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