Pinned Repositories
bacillus_eu07
Bioinformatics analysis to support manuscript submitted to Access Microbiology
coguk-follow-on-project
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-synteny
Generating synteny comparison between Foc TR4 genomes
fusarium-tr4-genomics
Genome sequence data reveal at least two distinct incursions of the Tropical Race 4 variant of Fusarium wilt into South America
get-viral-haplotypes
heterozygosity
Scripts used for profiling levels of heterozygosity over a genome sequence
xanthomonas-campestris-serbia
Supporting methods for Serbian Xcc paper
davidjstudholme's Repositories
davidjstudholme/fusarium-synteny
Generating synteny comparison between Foc TR4 genomes
davidjstudholme/xanthomonas-campestris-serbia
Supporting methods for Serbian Xcc paper
davidjstudholme/bacillus_eu07
Bioinformatics analysis to support manuscript submitted to Access Microbiology
davidjstudholme/coguk-follow-on-project
davidjstudholme/data
Repository for crowd-sourced data from genomics analysis of the UK ash dieback (Chalara fraxinea) outbreak 2012
davidjstudholme/dogma-to-tbl
Converting DOGMA annotation into NCBI's feature table format
davidjstudholme/extract-matching-reads-from-sam
Get mapped or non-mapped sequence read from SAM file
davidjstudholme/fusarium-tr4-genomics
Genome sequence data reveal at least two distinct incursions of the Tropical Race 4 variant of Fusarium wilt into South America
davidjstudholme/get-viral-haplotypes
davidjstudholme/heterozygosity
Scripts used for profiling levels of heterozygosity over a genome sequence
davidjstudholme/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.
davidjstudholme/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.
davidjstudholme/phylogenomics-xanthomonas-xv
davidjstudholme/pochonia
Chitosan induces differential transcript usage of chitosanase 3 encoding gene (csn3) in the biocontrol fungus Pochonia chlamydosporia 123
davidjstudholme/phytobacexplorer-curation
davidjstudholme/quick-and-dirty-16s
davidjstudholme/snp-comparator
I don't recommend that you use this. Use SnpEff instead.
davidjstudholme/snps-from-pileups
Script for inferring SNPs from pileup files
davidjstudholme/sort-genome-assemblies-by-host
Download bacterial genome assemblies and sort into folders according to BioProject 'host' field
davidjstudholme/xanthomonas-arboricola-serbia
davidjstudholme/xanthomonas-euvesicatoria-serbia
davidjstudholme/xanthomonas-phaseoli-serbia