Anthony Underwood's repositories
nf-core-bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
AMR
A free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods.
bioconda-recipes
Conda recipes for the bioconda channel.
configs
Config files used to define parameters specific to compute environments at different Institutions
datafunk
Miscellaneous data manipulation tools
fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases
hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
hladownload
A tool for downloading HLA alleles, epitopes and frequencies
MLSTar
An easy way of MLSTyping your genomes in R.
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
multi-package-containers
Testing building mulled containers for multi-requirement tools.
pangolin
Resources for a lineage naming scheme for SARS-CoV-2/hCoV-2019
pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
reproducible-research
A demonstration of how to work reproducibly using version control, containers, and a workflow manager.
test-datasets
Test data to be used for automated testing with the nf-core pipelines
tools
Python package with helper tools for the nf-core community.
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples