Fastv
Description
fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This tool supports both short reads (Illumina, BGI, etc.) and long reads (ONT, PacBio, etc.)
Environment Modules
Run module spider fastv to find out what environment modules are available for this application.
System Variables
- HPC_FASTV_DIR - installation directory
- HPC_FASTV_BIN - executable directory
Citation
If you publish research that uses fastv you have to cite it as follows:
Shifu Chen, Changshou He, Yingqiang Li, Zhicheng Li, Charles E Melancon III. A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data. bioRxiv 2020.05.12.092163; doi: https://doi.org/10.1101/2020.05.12.092163