This script filters low abundant reads from Bracken outputs directly. It will also remove relative abundance (Sample_frac) columns, taxonomy_id and taxonomic_lvl columns. Written in Bash.
You will need to specify -n as the lowest threshold for taxa to be removed. E.g. if you set -n 1000, if a specific taxon has less than 1000 reads across all samples, this taxon will be removed.
$ ./filter_bracken.sh -h
bracken-filter-reads filters low abundant reads from Bracken outputs
Usage example: bracken-filter-reads -n 1000 -o NEW-OUTPUT BRACKEN-OUTPUT-TABLE
Options:
-n Lowest threshold for filtering reads (default:1000)
-o New output name (default: OLDFILENAME-filtered)
-h Print usage and exit
-v Print version and exit
Version 0.1 (2021)
Author: Raymond Kiu [email protected]