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bacillus_eu07

Bioinformatics analysis to support manuscript submitted to Access Microbiology

cog-uk_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

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.

phylogenomics-xanthomonas-xv

phytobaccuration

pochonia

Chitosan induces differential transcript usage of chitosanase 3 encoding gene (csn3) in the biocontrol fungus Pochonia chlamydosporia 123

quickanddirty16s

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