Comparative analysis focused on E. muscae Berkeley strain. The primary genome annotation process is archived in Entomophthora_muscae_UCB github repository
This repository contains archive of code used to process the genomes on the UCR HPCC. The analysis include
- BUSCO run on species to compare completeness
- data captured for plotting the Nuclei metrics
- Hotpep runs for secretome prediction
- Ortholog analysis with OrthoFinder
- Telomere identification with pattern searches
- Repeat Induced Point mutations (RIP) analyses across species genomes
- Quantifying Transposons and Repetitive Element content
- Protein domain content (Pfam, CAZY with dbCAN, MEROPs) profiles across proteomes
The Supporting_data folder contains archives of transcriptome assemblies and data used to build multi-strain phylogeny.
Jason E Stajich, Brian Lovett, Emily Lee, Angie M. Macias, Ann E Hajek, Benjamin L de Bivort, Matt T. Kasson, Henrik H. De Fine Licht, Carolyn Elya. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. Submitted.
Curated by Jason Stajich - jason.stajich[AT]ucr.edu @hyphaltip