David Studholme's repositories
fusarium_synteny
Generating synteny comparison between Foc TR4 genomes
bacillus_EU07
Bioinformatics analysis to support manuscript submitted to Access Microbiology
data
Repository for crowd-sourced data from genomics analysis of the UK ash dieback (Chalara fraxinea) outbreak 2012
DOGMA_to_TBL
Converting DOGMA annotation into NCBI's feature table format
extract_matching_reads_from_sam
Get mapped or non-mapped sequence read from SAM file
fusarium_TR4_genomics
Genome sequence data reveal at least two distinct incursions of the Tropical Race 4 variant of Fusarium wilt into South America
heterozygosity
Scripts used for profiling levels of heterozygosity over a genome sequence
phylogenomics-Xanthomonas-1
Harrison, J., Hussain, R. M. F., Greer, S. F., Ntoukakis, V., Aspin, A., Vicente, J. G., Grant, M., & Studholme, D. J. (2023). Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiology, 5, acmi000532.v3.
phylogenomics-Xanthomonas-2
Harrison, J.; Hussain, R.M.F.; Aspin, A.; Grant, M.R.; Vicente, J.G.; Studholme, D.J. Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. Taxonomy 2023, 3, 29-45.
Pochonia
Chitosan induces differential transcript usage of chitosanase 3 encoding gene (csn3) in the biocontrol fungus Pochonia chlamydosporia 123
SNP_comparator
I don't recommend that you use this. Use SnpEff instead.
SNPsFromPileups
Script for inferring SNPs from pileup files
sort_genome_assemblies_by_host
Download bacterial genome assemblies and sort into folders according to BioProject 'host' field
Xanthomonas_campestris_Serbia
Supporting methods for Serbian Xcc paper