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bacterial_genomics_data_visualisation_tools

A curated list of data vis tools - mostly R based

bacterial_genomics_software_tools

Curated list of software tools for various aspects of prokaryote genomic analyses

convert_tsv_to_embl

Convert a tab separated regions file into embl format for use with remove_blocks_from_aln.py

flf_exemplar

genoparatyphi

Detect AMR mutations in Salmonella Paratyphi A genomes based on VCF or BAM files (mapped to Paratyphi A AKU_12601 reference genome)

lab_meeting_code_demos

Code demonstrations for Holt lab meeting 'show and tell' sessions

online-genomics-software-tools

A list of online resources for bacterial genomics

otustalker

OTUStalker is a small software tool designed to be compatible with QIIME (v1.8.0). Its purpose is to retrieve data pertinent to a single taxonomic group, from a larger (presumably mixed) data set, therefore allowing the user to concentrate their efforts on the specific taxa of interest. In effect, OTUStalker is taking the place of a targeted PCR primer set. OTUStalker requires a number of output files generated by QIIME (v1.8.0), and creates new files allowing re-analysis of the data set using QIIME.

phage_analysis_scripts

Tools for aggregating & analysing outputs from phage bioinformatics tools

png_styphi_2022

Scripts used for the analysis and visualisation of S. Typhi data from Papua New Guinea

r_project_template

Template repo for R-based analysis projects

snv_plotter

Plots the distribution of heterozygous and homozygous SNV calls from RedDog output

snv_stats_generator

SNV Quality Stats Generator provides summaries of high and low quality SNV calls from the GHRU mapping pipeline

team_scripts

shared code for collaborative data analyses