Main tool : Kraken2
Additional tools:
Full documentation: link to documentation
Kraken 2 is a fast and memory efficient tool for taxonomic assignment of metagenomics sequencing reads.
# query Illumina paired-end reads against kraken2 standard 8GB database
kraken2 --report test.kraken2.1.2.salmonella.report \
--output test.kraken2.1.2.salmonella.output \
--paired \
--db ./k2_standard_8gb_20210517 \
--threads 4 \
SRR10992628_1.gz SRR10992628_2.gz
# inspect a kraken2 database
kraken2-inspect --db ./k2_standard_8gb_20210517 --threads 4