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.