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Citations per year

Number of citations per year for the bioinformatics software tool Snippy

Tool usage distribution map

This map represents all the scientific publications referring to Snippy per scientific context
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Snippy specifications


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.
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
bwa mem, samtools, GNU parallel, freebayes, vcflib, vcftools, snpEff
Maintained Yes




No version available


Snippy citations


Clinically Relevant Plasmid Host Interactions Indicate that Transcriptional and Not Genomic Modifications Ameliorate Fitness Costs of Klebsiella pneumoniae Carbapenemase Carrying Plasmids

PMCID: 5915730
PMID: 29691332
DOI: 10.1128/mBio.02303-17
call_split See protocol

[…] order to look for SNPs and indels between the plasmid DNA sequences of pKpQIL-D2 (KY798506), ST258/pKpQIL-D2, and Ecl8/pKpQIL-D2 and of pKpQIL-UK (KY798507), ST258/pKpQIL-UK, and Ecl8/pKpQIL-UK, the snippy program was used ( […]


Emergence of Vancomycin Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

Sci Rep
PMCID: 5908837
PMID: 29674657
DOI: 10.1038/s41598-018-24614-6

[…] sequencing (WGS) were mapped to the annotated and publicly-available complete reference genome sequence of the E. faecium ST18 DO (TX16, NC017960) strain that was isolated in Texas, USA in 1998 using Snippy ( Contiguous consensus sequences (contigs) produced from reference mapping were used for the detection of single nucleotide polymorphisms (SNPs) relative to […]


Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology

Front Microbiol
PMCID: 5890179
PMID: 29662481
DOI: 10.3389/fmicb.2018.00596

[…] Single nucleotide polymorphisms (SNPs) calling was performed using the Snippy v2.6 pipeline. De novo assemblies of ST121 and ST14 genomes were analyzed separately. A newly generated draft genome for each L. monocytogenes ST was chosen as reference genome: LSALM51 for ST1 […]


Vancomycin resistant Enterococcus faecium sequence type 796 rapid international dissemination of a new epidemic clone

PMCID: 5863837
PMID: 29588851
DOI: 10.1186/s13756-018-0335-z
call_split See protocol

[…] were sequenced on the Illumina platform using either the MiSeq with 250-cycle paired end chemistry or the NextSeq 500 with 150-cycle paired end chemistry according to the manufacturer’s instructions.Snippy v3.2 ( was used to map sequence reads against the fully assembled Ef_aus0233 genome (GenBank accession no. PRJEB14733), a representative of the ST796 lineage […]


Expansion of a urethritis associated Neisseria meningitidis clade in the USA with concurrent acquisition of N. gonorrhoeae alleles

BMC Genomics
PMCID: 5834837
PMID: 29499642
DOI: 10.1186/s12864-018-4560-x

[…] of the 213 U.S. NmNG urethritis clade and closely related isolates. The alignment was generated by first calling consensus nucleotide sequences for each genome from Illumina short read data using the Snippy v3.1 pipeline [], which both mapped reads and called consensus nucleotides based on the complete, circular genome sequence of the closely related isolate M21273 as a reference. Genomes obtained […]


Isoniazid resistance levels of Mycobacterium tuberculosis can largely be predicted by high confidence resistance conferring mutations

Sci Rep
PMCID: 5818527
PMID: 29459669
DOI: 10.1038/s41598-018-21378-x
call_split See protocol

[…] outside of well-known drug resistance-related positions of the genome, whole genome sequences were assembled from the reads of the final set of 129 WHO-TDR strains and 47 Bangladesh isolates with the Snippy software (version 3.0). Snippy compares reads to the M. tuberculosis H37Rv reference genome (NC_000962.3),, employing the variant caller FreeBayes (version 0.9.21–7-g7dd41db). SNPs and indels f […]

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