Virlab's repositories
discover-virome
discover-virome: identify and quantify viruses from metagenomic assemblies
ena-upload
Snakemake workflow to upload Sars-Cov-2 reads to ENA
quantify-virome
quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
sarscov2-variation
SARS-CoV-2 sequencing workflow
virome-wrappers
snakemake wrappers
blast-virome
Virome taxonomic profiling using BLAST
cdhit
Automatically exported from code.google.com/p/cdhit
Demovir
Taxonomic classification of viruses at Order and Family level
minced
Mining CRISPRs in Environmental Datasets
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
dadasnake
Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
discover-profile
Snakemake HPC cluster profile for discover-virome workflow
DMP
Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)
emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
galaxy-api-scripts
Ad hoc scripts to run ARTIC COVID19 Galaxy workflows
mapto
Map reads to random stuff using bowtie2
quast-singularity
QUAST singularity image
sars-covid-2-ncbi
Download sars-covid-2 sequencing runs from NCBI
sarscov2-epidemiology
Visualisation of SARS-CoV-2 genomic epidemiology
singularity-cdhit
CD-HIT suite singularity image
virus-contigs-annotation
Virus contig annotation workflow