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1. PairedEndAssemblyConda PairedEndAssemblyConda Public

   Worflow performing de novo assembly of bacterial genomes from paired-end reads

   Python 1

2. PairedEndVariantConda PairedEndVariantConda Public

   Workflow performing variant calling analysis of bacterial genomes from paired-end reads

   Python 1

3. BashDataManagement BashDataManagement Public

   Useful Bash commands to manage genomics data and dataframes from multiple sources

   Shell 1

4. cgMLSTcomparison cgMLSTcomparison Public

   Script performing Principal Component Analysis (PCA) and Generalized Linear Model (GLM)

   R

5. DownsampledReads DownsampledReads Public

   Script performing 4-way figures and linear regressions

   R

6. TreeToCongruency TreeToCongruency Public

   Script comparing two trees through a tanglegram and estimations of congruency metrics

   R 1