Snippy protocols

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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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Snippy in pipelines

 (4)
2018
PMCID: 5770046
PMID: 29338017
DOI: 10.1371/journal.pone.0191042

[…] sequences generated were quality trimmed using trimmomatic v0.36 []. core snps were determined by mapping reads to the genome of s. enteritidis p125109 (genbank accession number nc_011294) using the snippy pipeline (https://github.com/tseemann/snippy), and identifying snps that were present in greater than 90% of reads at a depth of at least 10x. core snps were aligned and used to generate […]

2018
PMCID: 5801681
PMID: 29456969
DOI: 10.3389/fcimb.2018.00018

[…] resulting contigs were ordered using mauve 2.4.0 (darling et al., ) and strain mrsa252 as reference. the genome was annotated using prokka 1.12 (seemann, ). variant calling was performed using snippy v3.2 (seemann, ). the sequences reported in this paper have been deposited in the ncbi sequence read archive under bioproject number prjna414566., groups of data were statistically compared […]

2017
PMCID: 5381664
PMID: 28137745
DOI: 10.1093/gbe/evx003

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

2017
PMCID: 5686521
PMID: 29152586
DOI: 10.1128/mSystems.00127-17

[…] strain type, 2005) as a reference genome, we identified genetic differences (deletions [dels], indels, and snps) between the isolates and the reference strain (, ). core snps were identified using snippy and snippy-core (v 3.1) (). maximum-likelihood phylogeny was generated using phyml with the hky substitution model with bootstrapping (200×) (, ). to investigate the origin of a highly […]


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Snippy in publications

 (31)
PMCID: 5915730
PMID: 29691332
DOI: 10.1128/mBio.02303-17

[…] 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 (https://github.com/tseemann/snippy)., wgs data have been deposited in the european nucleotide archive (ena) project under accession number prjeb23315., citation buckner mmc, […]

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

[…] 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 (https://github.com/tseemann/snippy) was used to map sequence reads against the fully assembled ef_aus0233 genome (genbank accession no. prjeb14733), a representative of the st796 lineage […]

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

[…] 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 […]

PMCID: 5818527
PMID: 29459669
DOI: 10.1038/s41598-018-21378-x

[…] 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 […]

PMCID: 5801463
PMID: 29437920
DOI: 10.1128/mBio.02011-17

[…] between genome assemblies was assessed by ani and snps. ani was estimated by using mash version 1.1.1 with a k-mer size of 21 and a sketch size of 1,000 (), while snps were called by using snippy version 3.2 (bwa-mem version 0.7.15, freebayes version 1.0.2) (https://github.com/tseemann/snippy). all snps required a read depth of ≥10 reads with ≥90% of those aligned reads supporting […]


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