(A) Process Replicate Samples - FASTQ to VCF.ipynb
(B) Process Replicate Samples – Run Kraken on FASTQ.ipynb
(C) Retrieve SNPs between Replicate Pairs with AF change of 25% or more.ipynb
SNPs from Public Samples & tSNE Homoplasy Visualization
(A) Find Genomic Coordinates for Epitope Peptide Sequences using BLAST.ipynb
(B) Create Gene Categories.ipynb
(C) Process Replicate and Longitudinal Samples – Depth Extraction at Lineage Defining SNP sites for F2 Mixed Measure.ipynb
(D) Filter Replicate and Longitudinal Samples – Contamination with Kraken and F2 Mixed Measure.ipynb
(E) Process Replicate and Longitudinal Samples – Collect SNV Calls with Differing Alt AF between Sample Pairs.ipynb
(F) Code to Functionally Annotate Single Nucleotide Variants.ipynb
(G) PacBio Illumina Comparison - Empirical Base Pair Recall Score Positions to Drop.ipynb
(H) Filter Replicate and Longitudinal Samples – Contamination with Fixed SNP Threshold.ipynb
(I) Replicate and Longitudinal SNP comparison to find optimal AF change threshold% for in-host SNPs.ipynb
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