Name: Virlab
Type: Organization
Bio: Research Group of HIV Studies, Department of Microbiology, Faculty of Medicine, University of Tartu
Location: Biomedicum, Ravila 19, Tartu, 50411 Estonia
Blog: https://www.biomeditsiin.ut.ee/en/institute/department-microbiology
Virlab's Projects
16S rRNA amplicon sequencing analysis workflow using QIIME2
ARTIC nanopore protocol for nCoV2019 novel coronavirus
Virome taxonomic profiling using BLAST
Automatically exported from code.google.com/p/cdhit
Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
Taxonomic classification of viruses at Order and Family level
Snakemake HPC cluster profile for discover-virome workflow
discover-virome: identify and quantify viruses from metagenomic assemblies
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)
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
Snakemake workflow to upload Sars-Cov-2 reads to ENA
Ad hoc scripts to run ARTIC COVID19 Galaxy workflows
Install latest version of Aspera Connect and show example how to use it for downloading sequening data.
Map reads to random stuff using bowtie2
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
meta3c data analysis Snakemake workflow
MetaBat metagenome binning tool singularity image
Metagenomic binning based on Hi-C data
Mining CRISPRs in Environmental Datasets
Pathogen discovery pipeline (p-dip)
Phageterm fork of the code that is available via sourceforge
PRJNA399742 virome analysis samples list and config files
:zap: :aquarius: Rapid prokaryotic genome annotation
quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
QUAST singularity image