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CFSAN SNP Pipeline specifications


Unique identifier OMICS_14275
Name CFSAN SNP Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Reference-based alignments.
Input format FASTQ
Output data A matrix of SNPs for a given set of samples.
Output format TXT, FASTA, VCF, TSV
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.7.0
Stability Alpha
Java, Bowtie2, sra-toolkit, SAMtools, VarScan, BioPython
Maintained Yes




No version available



  • person_outline Errol Strain

Publication for CFSAN SNP Pipeline

CFSAN SNP Pipeline citations


A Validation Approach of an End to End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

Front Microbiol
PMCID: 5861296
PMID: 29593690
DOI: 10.3389/fmicb.2018.00446

[…] obtain pure colonies, extracting dna, performing short read sequencing with miseq illumina and carrying out bioinformatics analysis based on read mapping allowing identification of hqsnps with the cfsan snp pipeline. even though the cfsan snp pipeline was previously evaluated on its robustness and accuracy (davis et al., ), the end-to-end workflow has never been fully validated. the validation […]


Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms

Genome Biol Evol
PMCID: 5888409
PMID: 29617810
DOI: 10.1093/gbe/evy059

[…] dn/ds rates. these dn/ds rates were compared using mann–whitney u tests. additionally, we constructed maximum-likelihood bootstrapped trees from concatenated core snp alignments generated by the cfsan snp pipeline () with seaview (), and visualized with figtree (; last accessed march 21, 2018). the results of the breseq and cfsan pipelines differ […]


A Comprehensive Evaluation of the Genetic Relatedness of Listeria monocytogenes Serotype 4b Variant Strains

PMCID: 5601410
PMID: 28955706
DOI: 10.3389/fpubh.2017.00241

[…] 350 lm 4bv strains were identified from multiple parts of the usa as well as from australia and chile, dating back to 2001. the genomic relatedness of these strains was compared using the cfsan snp pipeline and multi-virulence-locus sequence typing (mvlst). using the cfsan pipeline tool, the 4bv strains were found to group into seven clusters that were separate from 4b strains. […]


Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, USA, 2013

Appl Environ Microbiol
PMCID: 5514676
PMID: 28550058
DOI: 10.1128/AEM.00633-17

[…] method or a specific snp-based method is also affected by the allele/snp calling algorithms. for example, an indel results in a different allele call by wgmlst, but it would not be counted by the cfsan snp pipeline unless at least one other isolate had an snp in that nucleotide position. the cfsan snp pipeline employs a filter to remove snps that may be the result of recombination […]


Whole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State

BMC Microbiol
PMCID: 5472956
PMID: 28619007
DOI: 10.1186/s12866-017-1043-1

[…] ]. however, using pacbio® may not be practical in every outbreak investigations. here, we explored the use of a clc genomics workbench-assembled draft genome (cfsan028853) as the reference for the cfsan snp pipeline and produced a wgs phylogeny that supported pfge and epidemiological evidence. we also tried cfsan028853 assembled by spades assembler 3.9.0 [], and the wgs analysis generated […]


Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

Front Microbiol
PMCID: 5440521
PMID: 28588568
DOI: 10.3389/fmicb.2017.00909

[…] as part of an outbreak under study. in the previous section, we introduced two main approaches to capture this variation: snv-based methods incorporated into pipelines such as the genometrakr’s cfsan snp pipeline (); and gene-by-gene methods incorporated into whole genome mlst-based pipelines such as bigsdb (). a third approach, referred to as alignment-free methods, trades accuracy […]

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CFSAN SNP Pipeline institution(s)
Biostatistics and Bioinformatics Staff, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA; Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA; Center for Food Safety and Applied Nutrition Scientific Engineering, Engility Corporation at FDA, Food and Drug Administration, College Park, MD, USA
CFSAN SNP Pipeline funding source(s)
This work was funded by the Center for Food Safety and Applied Nutrition, US FDA.

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