Merging
The merge
subcommand combines Kraken/Bracken output across several samples. It currently
supports
- Kraken output files (
*.k2
) - Bracken output files (
*.b2
) - 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.