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README.md

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These scripts and workflows were developed for comparative genomics of various Bordetella species isolates.

Most scripts are written in Perl with modest skill. All include brief documentation accessible by passing no parameters. Code in R is intended to be run interactively within Rstudio, it will not run without modifications to match your environment.

Included analysis workflows:

As described in Weigand et al. 2019 :

  1. WORKFLOW-Rearrangement.md: Exhaustive pairwise mauve alignment, clustering of colinear genomes, network analysis of select alignment pairs.
  2. WORKFLOW-InvertPrediction.md: Linear model of observed, symmetric inversions and prediction of potential inversions.

Additional pipelines:

Also described in Weigand et al. 2019

  1. Repeated kmer content:
  • kmer-frequency.sh
  • cdhit-plots.R
  1. Repeated gene content:
  • cds-frequency.sh
  • jellyfish-plots.R

Disclaimer

The contents of this repository are intended for research purposes only and come with no guarantees of their performance.

Analyses for publication were largely performed on a desktop computer with Ubuntu 14.04 LTS, perl v5.18.2, and R v3.4.4. See Weigand et al. 2019 for additional information.