Virlab
Research Group of HIV Studies, Department of Microbiology, Faculty of Medicine, University of Tartu
Biomedicum, Ravila 19, Tartu, 50411 Estonia
Pinned Repositories
blast-virome
Virome taxonomic profiling using BLAST
cdhit
Automatically exported from code.google.com/p/cdhit
discover-virome
discover-virome: identify and quantify viruses from metagenomic assemblies
ena-upload
Snakemake workflow to upload Sars-Cov-2 reads to ENA
metformin-virome
prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
quantify-virome
quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
sarscov2-variation
SARS-CoV-2 sequencing workflow
virfinder-test
Scripts to test and try virfinder package functionality
virome-wrappers
snakemake wrappers
Virlab's Repositories
hivlab/discover-virome
discover-virome: identify and quantify viruses from metagenomic assemblies
hivlab/ena-upload
Snakemake workflow to upload Sars-Cov-2 reads to ENA
hivlab/quantify-virome
quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
hivlab/sarscov2-variation
SARS-CoV-2 sequencing workflow
hivlab/virome-wrappers
snakemake wrappers
hivlab/blast-virome
Virome taxonomic profiling using BLAST
hivlab/cdhit
Automatically exported from code.google.com/p/cdhit
hivlab/Demovir
Taxonomic classification of viruses at Order and Family level
hivlab/metformin-virome
hivlab/minced
Mining CRISPRs in Environmental Datasets
hivlab/p-dip
Pathogen discovery pipeline (p-dip)
hivlab/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
hivlab/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
hivlab/ampliseq
16S rRNA amplicon sequencing analysis workflow using QIIME2
hivlab/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
hivlab/dadasnake
Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
hivlab/discover-profile
Snakemake HPC cluster profile for discover-virome workflow
hivlab/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)
hivlab/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
hivlab/ena-upload-cli
hivlab/galaxy-api-scripts
Ad hoc scripts to run ARTIC COVID19 Galaxy workflows
hivlab/mapto
Map reads to random stuff using bowtie2
hivlab/metaTOR
Metagenomic binning based on Hi-C data
hivlab/phageterm
Phageterm fork of the code that is available via sourceforge
hivlab/quast-singularity
QUAST singularity image
hivlab/sars-covid-2-ncbi
Download sars-covid-2 sequencing runs from NCBI
hivlab/sarscov2-epidemiology
Visualisation of SARS-CoV-2 genomic epidemiology
hivlab/singularity-cdhit
CD-HIT suite singularity image
hivlab/tools-iuc
Tool Shed repositories maintained by the Intergalactic Utilities Commission
hivlab/virus-contigs-annotation
Virus contig annotation workflow