In-host SNPs with AF change of 70% analyses
(A) Process Longitudinal Samples - FASTQ to VCF.ipynb
(B) Process Longitudinal Samples – Run Kraken on FASTQ.ipynb .ipynb
(C) Retrieve SNPs between Longitudinal Pairs with AF change of 25% or more.ipynb
(D) Retrieve SNPs between Longitudinal Pairs with AF change of 5% or more.ipynb
(E) Retrieve SNPs between Longitudinal Pairs with AF change of 70% or more.ipynb
(F) Num Heterozygous SNPs in First vs Second Sample in Treatment Failure Patients.ipynb
(G) Drug Resistance Genotype Prediction on Longitudinal Samples.ipynb
(H) Antibiotic Resistance Allele Dynamics.ipynb
(I) Antibiotic Resistance Allele Dynamics for Confirmed Failure Relapse Patients.ipynb
(J) Analyses on Time between Sampling for Mixed, Reinfection and Persistent Infections.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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