microbial_bioinformatics

Software tools for carrying out research in microbial bioinformatics

Tools:

> pangenome_analysis_pipeline

• Description:

  • Python script for carrying out pangenome analysis for microbial species including genome annotation

• Dependencies:

  • ETEtoolkit - ete-ncbiquery for NCBI taxonomy resource
  • prokka - microbial genome annotation (https://github.com/tseemann/prokka)
  • Roary - pangenome analysis pipeline (https://github.com/sanger-pathogens/Roary)
  • FastTree - building phylogenetic trees ()

• Usage:

  • executed by main.py file
  • species fasta genome sequences to be downloaded in folders (folder name = species name) situated in the root directory
  • output: files in the pangenome_analysis directory created during script execution

> pangenome_analysis_pipeline_v03

• Description:

  • Python script for carrying out pangenome analysis for microbial species

• Dependencies:

  • ETEtoolkit - ete-ncbiquery for NCBI taxonomy resource
  • prokka - microbial genome annotation (https://github.com/tseemann/prokka)
  • Roary - pangenome analysis pipeline (https://github.com/sanger-pathogens/Roary)
  • ete3 - A Python framework for the analysis and visualization of trees. (http://etetoolkit.org/)

• Usage:

  • executed by main.py file

> panGWAS_v01

• Description:

  • Python scripts for carrying out microbial Genome Wide Association Studies using pangenome analysis

• Dependencies:

  • ETEtoolkit - ete-ncbiquery for NCBI taxonomy resource
  • prokka - microbial genome annotation (https://github.com/tseemann/prokka)
  • Roary - pangenome analysis pipeline (https://github.com/sanger-pathogens/Roary)
  • Scoary - bacterial GWAS (https://github.com/AdmiralenOla/Scoary)
  • SciPy - Python-based ecosystem of open-source software for mathematics, science, and engineering.
  • ete3 - A Python framework for the analysis and visualization of trees. (http://etetoolkit.org/)

• Usage:

  • executed by main.py file
  • phenotypic data file should be placed in primary_data dir. Write a function that returns a pandas dataFrame of index = tax_id;
  • output: reulsts files in scoary_dir created upon scipt execution