A client-side WebAssembly pipeline for viral consensus sequence calling.
Visit: https://niema-lab.github.io/ViralWasm-Consensus/ to run the pipeline.
Prerequisites: Python (Can be downloaded here: https://www.python.org/downloads/)
To run the pipeline locally without internet, download the zip file containing the offline mode of ViralWasm-Consensus: https://github.com/Niema-Lab/ViralWasm-Consensus/raw/master/viralwasm-consensus-offline.zip. After, extract the folder, and right click on the run_website.py file and select "Open with Python" for Windows or "Open With -> Python Launcher" for Mac.
Note: When starting the website for the first time offline, you may be prompted with a firewall warning. Click "Allow Access" to run the pipeline.
If you use ViralWasm-Consensus in your work, please cite:
Ji D, Aboukhalil R, Moshiri N (2023). "ViralWasm: a client-side user-friendly web application suite for viral genomics." Bioinformatics. btae018. doi:10.1093/bioinformatics/btae018
Please also cite the following tools used in ViralWasm-Epi:
See https://biowasm.com/.
Moshiri N (2023). "ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data." Bioinformatics. btad317. doi:10.1093/bioinformatics/btad317
Li H (2018). "Minimap2: pairwise alignment for nucleotide sequences." Bioinformatics. 34(18):3094–3100. doi:10.1093/bioinformatics/bty191
Chen S, Zhou Y, Chen Y, Gu J (2018). "fastp: an ultra-fast all-in-one FASTQ preprocessor." Bioinformatics. 34(17):i884–i890. doi:10.1093/bioinformatics/bty560