Skip to content

Merging

The merge subcommand combines Kraken/Bracken output across several samples. It currently supports

  1. Kraken output files (*.k2)
  2. Bracken output files (*.b2)
  3. Mapping analyses (*.csv)

Info

architeuthis will automatically recognize and validate the file type and tell you if your file is not supported.

Usage

For instance to combine several Bracken output files:

architeuthis merge -o bracken_merged.csv *.b2

This will combine all *.b2 files into a single merged CSV with an additional sample_id column generated from the basename of the files.

For Kraken output the resulting file will still be in the native Kraken output format without an additional column as this format operates on individual reads which already have a unique sample-specific ID.