CFSAN SNP Pipeline pipeline

CFSAN SNP Pipeline specifications

Information


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
Requirements Java, Bowtie2, sra-toolkit, SAMtools, VarScan, BioPython
Maintained Yes

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Maintainer


  • person_outline Errol Strain <>

Publication for CFSAN SNP Pipeline

CFSAN SNP Pipeline citation

2017
PMCID: 5413027

[…] available in s1 table., the genome assemblies were analyzed using the jspecies tetranucleotide frequency tool as previously described [10, 26]. additionally, the sra files were analyzed using the cfsan snp pipeline [27] with cfsan023463 as the reference genome (table 1). this strain was isolated from peaches associated with the initial incident linked to stone fruits and its genome sequence […]

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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