CFSAN SNP Pipeline specifications

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

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CFSAN SNP Pipeline distribution

download

CFSAN SNP Pipeline support

Documentation

Maintainer

  • Errol Strain <>

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Publications

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

Funding source(s)

This work was funded by the Center for Food Safety and Applied Nutrition, US FDA.

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