CFSAN SNP Pipeline protocols

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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



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  • person_outline Errol Strain <>

Publication for CFSAN SNP Pipeline

CFSAN SNP Pipeline in pipelines

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

[…] closure of the genome by circlator (hunt et al., ) and final polishing by quiver v1 (pacific biosciences)., high quality snp pipeline developed by the center for food safety and applied nutrition (cfsan snp pipeline v.1.0.0/fda) was used for snp calling on l. monocytogenes and s. enterica isolates (davis et al., ). the reference genome was either a genome generated by pacbio assembly, a public […]

PMCID: 5413027
PMID: 28464038
DOI: 10.1371/journal.pone.0176912

[…] numbers are available in ., the genome assemblies were analyzed using the jspecies tetranucleotide frequency tool as previously described [, ]. additionally, the sra files were analyzed using the cfsan snp pipeline [] with cfsan023463 as the reference genome (). this strain was isolated from peaches associated with the initial incident linked to stone fruits and its genome sequence is closed […]

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CFSAN SNP Pipeline in publications

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 […]

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 […]

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. […]

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 […]

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 […]

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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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