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Revision 36e27011b5cfaed00521a38652fe2dc853832f25 authored by vargasr39 on 03 February 2021, 06:53:51 UTC, committed by GitHub on 03 February 2021, 06:53:51 UTC 
Update README.md
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Longitudinal Isolates
Replicate Isolates
SNPs from Public Samples & tSNE Homoplasy Visualization
Short Read Simulations
(A) Find Genomic Coordinates for Epitope Peptide Sequences using BLAST.ipynb -rw-r--r-- 121.1 KB
(B) Create Gene Categories.ipynb -rw-r--r-- 13.5 KB
(C) Process Replicate and Longitudinal Samples – Depth Extraction at Lineage Defining SNP sites for F2 Mixed Measure.ipynb -rw-r--r-- 78.6 KB
(D) Filter Replicate and Longitudinal Samples – Contamination with Kraken and F2 Mixed Measure.ipynb -rw-r--r-- 282.1 KB
(E) Process Replicate and Longitudinal Samples – Collect SNV Calls with Differing Alt AF between Sample Pairs.ipynb -rw-r--r-- 125.0 KB
(F) Code to Functionally Annotate Single Nucleotide Variants.ipynb -rw-r--r-- 33.0 KB
(G) PacBio Illumina Comparison - Empirical Base Pair Recall Score Positions to Drop.ipynb -rw-r--r-- 33.8 KB
(H) Filter Replicate and Longitudinal Samples – Contamination with Fixed SNP Threshold.ipynb -rw-r--r-- 337.2 KB
(I) Replicate and Longitudinal SNP comparison to find optimal AF change threshold% for in-host SNPs.ipynb -rw-r--r-- 219.0 KB
README.md -rw-r--r-- 3.5 KB

README.md

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