Today, I want to introduce my new work, fastv, an ultra-fast tool for detecting viral sequence from sequencing data for detection of viral infectious diseases, like COVID-19.
This tool accepts the input of raw or clean FASTQ files (both SE/PE), performs quality filtering as fastp does (cut adapters, remove low quality reads, correct wrong bases), and then scans the clean data for the viral sequences.
take a quick glance of the informative report
try fastv to generate above reports
./fastv -i testdata.fq.gz
./fastv -i R1.fq.gz -I R2.fq.gz
For more information, go: github.com/OpenGene/fastv