Barena

Barena is a tool to filter FASTQ reads by taxon using Kraken2 classification output.

Usage

Basic filtering

Filter reads matching taxon 9606:

barena -1 reads_R1.fq.gz -2 reads_R2.fq.gz -k kraken.out -t 9606 -o output_dir

Filtering with descendants

To include all children of a taxon, provide the kraken2-inspect output:

barena -1 reads.fq -k kraken.out -t 9606 --child -d inspect.txt -c human_reads.fq.gz

Streaming from Kraken2

kraken2 --db DB reads.fq | barena -1 reads.fq -t 9606 -o human_only

Options

• -1, --r1: FASTQ file (R1)
• -2, --r2: FASTQ file (R2)
• -k, --kraken: Kraken2 raw output (default: stdin)
• -d, --inspect-db: Kraken2-inspect output (required for --child)
• -t, --taxon: Taxon ID to match (can be repeated)
• --child: Include descendants of the specified taxons
• -o, --outdir: Output directory for classified/unclassified reads