The goal of VirusWarn-SC2 is to detect SARS-CoV-2 emerging variants from collected bases of genomes, before their annotation by phylogenetic analysis. It does so by parsing SARS-CoV-2 genomes and detecting amino acids mutations in the spike proteins that can be associated with a phenotypic change. The phenotypic changes are annotated according to the knowledge accumulated on previous variants. Owing to the limited size of the genome, convergent evolution is expected to take place.
VirusWarn-SC2 is part of VirusWarn
For more information take a look at the VirusWarn-SC2 Documentation
To run the pipeline, you need to have conda and Nextflow installed and set up.
All other dependencies will be installed over conda in the pipeline.
To install conda, use the following bash commands if you are working on Linux:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.shTo install conda, use the following bash commands if you are working on Mac:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh
bash Miniconda3-latest-MacOSX-arm64.shThen, Nextflow an be installed over conda:
conda create -n nextflow -c bioconda nextflow
conda activate nextflowThe VOCAL repository can be cloned from Git:
git clone https://github.com/rki-mf1/VirusWarn-SC2.gitnextflow run main.nf --helpnextflow run main.nf \
-profile conda,local \
--fasta 'test/sample-test.fasta'nextflow run main.nf \
-profile conda,local \
--fasta 'test/sample-test.fasta' \
--metadata 'test/meta.tsv' \
--psl- ID column (match with sample ID in FASTA file)
- LINEAGE column (e.g., B.1.1.7, BA.1)
🐌 Slow?: The alignment option in VOCAL uses a biopython pairwise aligner and can be relatively slow. It is thus recommended to first generate an alignment file of all the sequences before running VOCAL annotation of the mutations. The alignment file (in PSL format) can be created using the tool pblat by adding the option --psl.
nextflow run main.nf \
-profile conda,local \
--fasta 'test/sample-test.fasta' \
--pslVirusWarn-SC2 is run without option --psl, it realigns each query sequence to the reference sequence Wuhan NC_045512 using the pairwise alignment function in the biopython library.
fasta REQUIRED! The path to the fasta file with the sequences for VirusWarn-SC2.
[ default: '' ]
metadata The path to a metadate file for the sequences.
[ default: '' ]
year Specify the year from which the information should
be used for the ranking.
[ default: 2022 ]
psl Run process with pblat alignment.
[ default: false ]
strict Run process with strict alert levels (without orange).
[ default: 'n' ]
VirusWarn-SC2 output an alert level in four different colours which can be classified into 3 ratings.
| Alert color | Description | Impact |
|---|---|---|
| Pink | Variant is known as VOC/VOI and containing MOC or new mutations. | HIGH |
| Red | Not VOC/VOI but contain high MOC or ROI, and a new matuation (likely to cause a problem/ new dangerous). | HIGH |
| Orange | Variant contains moderately muations, or also possibly consider them either VUM or De-escalated variant. | MODERATE |
| Grey | Near-zero mutation size for MOC or ROI or either no MOC or no ROI. | LOW |
Did you find a bug? 🐛 Suggestion/Feedback/Feature request? 👨💻 Please visit GitHub Issues
For business inquiries or professional support requests 🍺 Please feel free to contact us!
-
Original Idea: SC2 Evolution Working group - M. von Kleist, S. Clavignac-Spencer
-
Funding: Supported by the European Centers for Disease Control [grant number ECDC GRANT/2021/008 ECD.12222].