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albugo

Commands used in the assembly and annotation of Albugo genomes

alternaria

Scripts used for the analysis of Alternaria genomes

ananassa_diversity

ananassa_qtl

Bioinformatics pipelines used to analyse disease resistance QTL in cultivated strawberry

bioinformatics_tools

Tools used in the analysis of high-throughput sequencing data

cassava

Commands used in the analysis of cassava genotyping data

clocks

codon_analysis

The folder contains scripts used to perform codon analysis and mainly used for Fusarium venenatum

colletotrichum_gloeosporioides

Commands used in the analysis of Colletotrichum Gleosporoides genomes

cydia

Cydia genomics

didymella

Commands used in the assembly and analysis of Didymella genomes

ensa

frankia

fusarium

Fusarium Genomics

fusarium_ampseq

Commands used in analysis of amplicon sequence data of Fusarium infested soil samples and artificial mixes.

fusarium_comp

Comparative genomics of fusarium RJH

fusarium_ex_narcissus

Commands used in the analysis of Fusarium oxysporum isolates ex. narcissus

fusarium_ex_pea

Commands used in the analysis of Fusarium oxysporum isolates ex. pea

fusarium_ex_strawberry

Commands used in the analysis of Fusarium oxysporum isolates ex. strawberry.

fusarium_species

Analysis of fusarium species and F. oxysporum species complex

fusarium_venenatum

Bioinformatic analysis of fusarium venenatum genomes

fv_c-variants

Detection SNPs leading to branching variants of Fv

fv_metabolite_expression

Differential expression of Fv secondary metabolite pathways

hop_genomics

magnaporthe

Commands used in the analysis of Magnaporthe genomes

mapping

metabarcoding_projects

Metabarcoding projects

metagenomics

Analysis of Xiangming's metagenome data

metarhizium

Metarhizium genomics

nano_diagnositcs

Documentation of analyses and commands used as part of the PhD project investigating next generation diagnostics