Standalone example output from the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) https://github.com/jaleezyy/covid-19-signal
Nasir et al. SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes. Manuscript in preparation.
To demonstrate SIGNAL output and applicability, we re-examined a dataset of 113 Canadian samples from November 6-10, 2020 that underwent ARTIC3 PCR and Illumina paired-end 250 bp sequencing. All sequencing reads are available in BioProject PRJNA689621. All consensus genome sequences and associated metadata in this dataset are published in GISAID’s EpiCoV database: to view the contributors of each individual sequence with details such as accession number, Virus name, Collection date, Originating Lab and Submitting Lab and the list of Authors, visit DOI:10.55876/gis8.240105tb.
To download the demonstration dataset, run the following provided script as followed:
bash download_bioproject.sh -i PRJNA689621 -o benchmark_input -f E
You can replace the value for -o to any path on the filesystem.
To just view and output (TSV) the relevant accession IDs, add -l to the above command.
Upon downloading SIGNAL and its correspoding data dependancies, configuration files can then be generated using the created directory as input:
python signalexe.py -d benchmark_input --add-breseq --config-only
All individual processes within SIGNAL can then be executed using the following command:
python signalexe.py -c benchmark_input_config.yaml --cores 4 all postprocess
Replace the value for -c as needed. If the ncov-tools directory can be found within the SIGNAL root, ncov_tools can be appended to the end of the above command.
Additional benchmarking datasets and their outputs are provided here covering a wide array of scenarios. General description and downloading instructions of datasets can be found on the CDCGov Repository.
- SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) version v1.6.6
- PANGOLIN versions
- NextClade versions