Thomas Battenfeld's repositories
document-anonymization
Personal data redaction on images based on FHIR patient resources.
sars-dashboard
Dashboard to browse analyses created by UnCoVar.
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
bioconda-recipes
Conda recipes for the bioconda channel.
etc
Code snippets, cheatsheets and other stuff
mkdocs
Project documentation with Markdown.
ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
peppy-feedstock
A conda-smithy repository for peppy.
release-please-action
automated releases based on conventional commits
rl_bin_packing
Packing bins with reinforcement learning
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
rust-bio-tools
A set of command line utilities based on Rust-Bio.
sars-cov-2-wbe
Quantifying SARS-CoV-2 lineage abundances in wastewater.
snakelines
Computational pipelines for processing of paired-end Illumina reads
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
snakemake-github-action
A Github action for running a Snakemake workflow
snakemake-workflow-catalog
A statically generated catalog of available Snakemake workflows
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
uncovar
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes