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.). See: https://github.com/OpenGene/fastv

Three simple steps to identify viruses from mNGS FASTQ data:
1, Install fastv.
wget http://opengene.org/fastv/fastv
chmod a+x ./fastv
You can also get fastv by compiling from source code.

2, Download the k-mer collection file:
wget http://opengene.org/viral.kc.fasta.gz

3, Run fastv with your FASTQ data (usually takes less than 5 minutes)
./fastv -i filename.fastq.gz -c viral.kc.fasta.gz

Once finished, check the results in fastv.html and fastv.json

* If you also want to identify both viruses and microorganisms, use http://opengene.org/microbial.kc.fasta.gz to replace http://opengene.org/viral.kc.fasta.gz

参考：
https://www.biostars.org/p/439805/

https://github.com/OpenGene/