Pan-genome analyses of model Fungal species.

Charley G. P. McCarthy & David A. Fitzpatrick (2019). Microbial Genomics 5(2). doi: 10.1099/mgen.0.000243. Link.

Please note: I have rewritten these pipelines entirely and incorporated more analysis and functions (along with nicer code) into what's now known as Pangloss.

This repository holds custom pipelines used to analyse the pan-genomes of four model fungal species; Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus.

The pipelines are as follows:

• A custom gene model prediction pipeline which uses parallelized Exonerate searches, GeneMark-ES HMM prediction and TransDecoder coding potential prediction to generate gene model sets for each strain genome in a pan-genome dataset.

• A post-processing pipeline which takes the results of PanOCT output and attempts to merge non-core syntenic clusters of gene models which have reciprocal sequence similarity between each other but have otherwise lost microsynteny using iterative BLAST+ searches and parsing. This pipeline also runs two R scripts to generate ring charts of the size of species core and accessory genomes as well as an UpSet distribution of accessory gene model clusters within pan-genomes.

Requirements

Each analysis in McCarthy & Fitzpatrick (2019) using these pipelines was performed on a HPC cluster with a PBS scheduler. These pipelines have also been tested in other Linux and macOS environments.

• Python

  • Biopython

• R

  • Cairo
  • UpSetR
  • ggplot2
  • ggrepel

• BLAST+

• Exonerate

• GeneMark-ES

• TransDecoder