/PerMutation

Code and programs developed for Tn-Seq analysis of E. faecalis MMH594.

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

PerMutation

Code for Tn-Seq analysis of E. faecalis MMH594. Check out the wiki more details:

  1. Processing, Mapping, Replication Bias Correction, and Normalization Across Replicates
  2. Assessing the Fitness Cost of Genes For Growth on Nutrient Rich Media
  3. Predicting Whether Genes Contribute to Antibiotic Resistance

All programs/scripts written in Python-3, no real installation required. Python-3 libraries used include:

  • biopython
  • numpy
  • scipy
  • pysam

For processing and mapping of sequencing data to the reference genome the following third-party tools are necessary:

  • trimmomatic
  • samtools
  • bowtie2
  • fastx_toolkit

Progams should work if the user creates and uses a conda environment from the provided yml file.