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.) Modules system sets up the following environment variables for this module:

Environment Modules¶

Run module spider fastv to find out what environment modules are available for this application.

Environment Variables¶

HPC_FASTV_DIR - installation directory
HPC_FASTV_BIN - executable directory

Categories¶

bioinformatics, sequencing