Snippy pipeline

Snippy specifications

Information


Unique identifier OMICS_03551
Name Snippy
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

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Maintainer


  • person_outline Torsten Seemann <>

Snippy IN pipelines

 (2)
2017
PMCID: 5381664
PMID: 28137745
DOI: 10.1093/gbe/evx003

[…] that no single method is optimal, whereas multiple approaches may maximize the chances of detecting recombination events (posada and crandall 2001). a whole genome alignment was constructed with snippy using default parameters. recombination was assessed using the pairwise homoplasy index test φw (bruen et al. 2006) (with significance set at 0.05), as implemented in splitstree v 4.13.1 […]

2017
PMCID: 5635451
PMID: 29056927
DOI: 10.3389/fmicb.2017.01906

[…] 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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