jpayne@0: jpayne@0: Build SNP table in VCF format from fastq collections jpayne@0: jpayne@0: bowtie2 jpayne@0: smalt jpayne@0: samtools jpayne@0: picard jpayne@0: varscan jpayne@0: tabix jpayne@0: bgzip jpayne@0: fastq-dump jpayne@0: biopython jpayne@0: snp-pipeline jpayne@0: jpayne@0: &2 jpayne@0: && source ./snp-unwind.sh jpayne@0: ]]> jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: jpayne@0: The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. jpayne@0:

jpayne@0: The SNP Pipeline was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition. jpayne@0:

jpayne@0: Free software. jpayne@0: Documentation: http://snp-pipeline.readthedocs.io/en/latest/readme.html jpayne@0: Source Code: https://github.com/CFSAN-Biostatistics/snp-pipeline jpayne@0: PyPI Distribution: https://pypi.python.org/pypi/snp-pipeline jpayne@0: ]]> jpayne@0: jpayne@0: 10.7717/peerj-cs.20 jpayne@0: jpayne@0: @misc{cfsan-snp-pipeline, jpayne@0: author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain}, jpayne@0: year = {2015}, jpayne@0: title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data}, jpayne@0: url = {https://doi.org/10.7717/peerj-cs.20}, jpayne@0: journal = {PeerJ Computer Science}, jpayne@0: } jpayne@0: jpayne@0: