README.md

Kraken2 2.1.3 container

Main tool : Kraken2

Additional tools:

• Pre-built kraken2 databases can be found here

Full documentation: link to documentation

Kraken 2 is a fast and memory efficient tool for taxonomic assignment of metagenomics sequencing reads.

Example Usage

# 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