Reference genome database for Kraken 2
======

Kraken 2 is a k-mer-based taxonomic classifier for metagenomic data.

 - Website: https://ccb.jhu.edu/software/kraken2/
 - Citation: Wood DE, Lu J, Langmead B. Improved metagenomic analysis with
   Kraken 2. Genome biology. 2019. 20(1):257.

Built using Kraken 2 v2.1.2. Command:

```
kraken2-build --threads # --build --db .
```

The default taxonomy is built-in. See: ../../taxonomy/.

Typical classification commands:

Single FASTA file, mapping only:
```
kraken2 --threads # --db . input.fa > output.tsv
```

Paired-end FASTQ files, mapping and report (taxonomic profile):
```
kraken2 --threads # --db . --paired input.R1.fq input.R2.fq \
  --report report.txt --output output.tsv
```

This analysis requires at least 75 GB memory.