├── .gitignore ├── .travis.yaml ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── Dockerfile ├── HISTORY.rst ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.rst ├── docs ├── DenseSnps.png ├── DenseSnps.xlsx ├── Makefile ├── SnpPipelineDataFlow.png ├── SnpPipelineDataFlow.vsd ├── _static │ └── theme_overrides.css ├── authors.rst ├── cmd_ref.rst ├── conf.py ├── configuration.rst ├── contributing.rst ├── dataflow.rst ├── faq.rst ├── history.rst ├── index.rst ├── installation.rst ├── make_cmd_reference.sh ├── readme.rst ├── reproducible.rst └── usage.rst ├── environment.yml ├── scripts ├── alignSampleToReference.sh ├── calculate_snp_distances.py ├── call_consensus.py ├── collectSampleMetrics.sh ├── combineSampleMetrics.sh ├── copy_snppipeline_data.py ├── create_snp_list.py ├── create_snp_matrix.py ├── create_snp_reference_seq.py ├── mergeVcf.sh ├── prepReference.sh ├── prepSamples.sh ├── run_snp_pipeline.sh └── snp_filter.py ├── setup.py ├── snppipeline ├── __init__.py ├── call_consensus.py ├── call_sites.py ├── cfsan_snp_pipeline.py ├── collect_metrics.py ├── combine_metrics.py ├── command.py ├── data.py ├── data │ ├── README │ ├── agonaExpectedResults │ │ ├── metrics.tsv │ │ ├── referenceSNP.fasta │ │ ├── referenceSNP_preserved.fasta │ │ ├── samples │ │ │ ├── ERR178926 │ │ │ │ ├── consensus.fasta │ │ │ │ └── var.flt.vcf │ │ │ ├── ERR178929 │ │ │ │ ├── consensus.fasta │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1566386 │ │ │ │ ├── consensus.fasta │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR2566901 │ │ │ │ ├── consensus.fasta │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR3664651 │ │ │ │ ├── consensus.fasta │ │ │ │ └── var.flt.vcf │ │ │ └── SRR3665129 │ │ │ │ ├── consensus.fasta │ │ │ │ └── var.flt.vcf │ │ ├── snp_distance_matrix.tsv │ │ ├── snp_distance_matrix_preserved.tsv │ │ ├── snp_distance_pairwise.tsv │ │ ├── snplist.txt │ │ ├── snplist_preserved.txt │ │ ├── snpma.fasta │ │ ├── snpma.vcf │ │ ├── snpma_preserved.fasta │ │ └── snpma_preserved.vcf │ ├── agonaInputs │ │ ├── reference │ │ │ └── NC_011149.fasta │ │ ├── sampleList │ │ └── sha256sumCheck │ ├── configuration │ │ └── snppipeline.conf │ ├── lambdaVirusExpectedResults │ │ ├── metrics.tsv │ │ ├── referenceSNP.fasta │ │ ├── referenceSNP_preserved.fasta │ │ ├── samples │ │ │ ├── sample1 │ │ │ │ ├── consensus.fasta │ │ │ │ ├── consensus.vcf │ │ │ │ ├── consensus_preserved.fasta │ │ │ │ ├── consensus_preserved.vcf │ │ │ │ ├── metrics │ │ │ │ ├── reads.all.pileup │ │ │ │ ├── reads.sam │ │ │ │ ├── var.flt.vcf │ │ │ │ ├── var.flt_preserved.vcf │ │ │ │ └── var.flt_removed.vcf │ │ │ ├── sample2 │ │ │ │ ├── consensus.fasta │ │ │ │ ├── consensus.vcf │ │ │ │ ├── consensus_preserved.fasta │ │ │ │ ├── consensus_preserved.vcf │ │ │ │ ├── metrics │ │ │ │ ├── reads.all.pileup │ │ │ │ ├── reads.sam │ │ │ │ ├── var.flt.vcf │ │ │ │ ├── var.flt_preserved.vcf │ │ │ │ └── var.flt_removed.vcf │ │ │ ├── sample3 │ │ │ │ ├── consensus.fasta │ │ │ │ ├── consensus.vcf │ │ │ │ ├── consensus_preserved.fasta │ │ │ │ ├── consensus_preserved.vcf │ │ │ │ ├── metrics │ │ │ │ ├── reads.all.pileup │ │ │ │ ├── reads.sam │ │ │ │ ├── var.flt.vcf │ │ │ │ ├── var.flt_preserved.vcf │ │ │ │ └── var.flt_removed.vcf │ │ │ └── sample4 │ │ │ │ ├── consensus.fasta │ │ │ │ ├── consensus.vcf │ │ │ │ ├── consensus_preserved.fasta │ │ │ │ ├── consensus_preserved.vcf │ │ │ │ ├── metrics │ │ │ │ ├── reads.all.pileup │ │ │ │ ├── reads.sam │ │ │ │ ├── var.flt.vcf │ │ │ │ ├── var.flt_preserved.vcf │ │ │ │ └── var.flt_removed.vcf │ │ ├── snp_distance_matrix.tsv │ │ ├── snp_distance_matrix_preserved.tsv │ │ ├── snp_distance_pairwise.tsv │ │ ├── snp_distance_pairwise_preserved.tsv │ │ ├── snplist.txt │ │ ├── snplist_preserved.txt │ │ ├── snpma.fasta │ │ ├── snpma.vcf │ │ ├── snpma_preserved.fasta │ │ └── snpma_preserved.vcf │ ├── lambdaVirusInputs │ │ ├── README │ │ ├── reference │ │ │ └── lambda_virus.fasta │ │ └── samples │ │ │ ├── sample1 │ │ │ ├── sample1_1.fastq │ │ │ └── sample1_2.fastq │ │ │ ├── sample2 │ │ │ ├── sample2_1.fastq │ │ │ └── sample2_2.fastq │ │ │ ├── sample3 │ │ │ ├── sample3_1.fastq │ │ │ └── sample3_2.fastq │ │ │ └── sample4 │ │ │ ├── sample4_1.fastq │ │ │ └── sample4_2.fastq │ ├── listeriaExpectedResults │ │ ├── metrics.tsv │ │ ├── referenceSNP.fasta │ │ ├── referenceSNP_preserved.fasta │ │ ├── samples │ │ │ ├── SRR1553725 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553739 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553740 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553750 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553756 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553764 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553773 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553774 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553779 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553784 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553788 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553791 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553792 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553796 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553797 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553798 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553804 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553816 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553820 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553821 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553826 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553827 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553840 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553850 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553851 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553855 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553856 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553866 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553867 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553871 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553882 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553906 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1553907 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1554256 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1554259 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556285 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556286 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556287 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556288 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556289 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556290 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556291 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556292 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556293 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556294 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556295 │ │ │ │ └── var.flt.vcf │ │ │ ├── SRR1556296 │ │ │ │ └── var.flt.vcf │ │ │ └── SRR1556297 │ │ │ │ └── var.flt.vcf │ │ ├── snp_distance_matrix.tsv │ │ ├── snp_distance_matrix_preserved.tsv │ │ ├── snp_distance_pairwise.tsv │ │ ├── snplist.txt │ │ ├── snplist_preserved.txt │ │ ├── snpma.fasta │ │ └── snpma_preserved.fasta │ └── listeriaInputs │ │ ├── reference │ │ └── CFSAN023463.HGAP.draft.fasta │ │ ├── sampleList │ │ └── sha256sumCheck ├── distance.py ├── fastq.py ├── filter_regions.py ├── index_ref.py ├── map_reads.py ├── merge_sites.py ├── merge_vcfs.py ├── pileup.py ├── purge.py ├── run.py ├── snp_matrix.py ├── snp_reference.py ├── utils.py 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