Joon Klaps's repositories
viralgenie
Detect iSNV and construct whole viral genomes from metagenomic samples
bioconda-recipes
Conda recipes for the bioconda channel.
configs
Config files used to define parameters specific to compute environments at different Institutions
kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
lasvphylo
An nextflow pipeline for making LASV alignments
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
suppl_bacteroides_fragilis
Supplementary information with the article 'Large-scale genomic characterisation of Bacteroides fragilis reveals multiple functionally divergent lineages and a distinct species.'
multi-package-containers
Testing building mulled containers for multi-requirement tools.
nextclade_data
Datasets for https://github.com/nextstrain/nextclade
nextcloud_share_url_downloader
Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.
Nextflow_sandbox
A playground to explore how to implement things in Nextflow and nf-core
phageannotator
Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
tools
Python package with helper tools for the nf-core community.
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
website-nf-core
Code and files for the main nf-core website.