TENTAKKL

Taxonomic Extraction Normalization Transformation and Accounting for Kraken/bracKen fiLes

Introduction

This is a pre-beta release. It's probably not suitable for your purposes yet...

kraken2 and bracken are highly-cited tools for classifying short read data and generating relative abundances.

This tool reads bracken (and kraken) report files and performs a variety of operations.

tentakkl:

• Supports user-selectable target taxa (reads are aggregated to parent taxonomic nodes)
• Supports user-selectable taxa to remove from the report
• Recovers reads lost by bracken (reported in STDOUT as "reads discarded" and "reads not distributed")
• Recovers unclassified reads from the kraken2 reports
• Supports output of raw counts, normalization to bracken (~classified reads) or normalization to kraken2 (~classified+unclassified)
• Supports list (tidy) and wide (Excel-compatible) outputs

16:45 biowulf minitax$ perl -w tentakkl.pl 
TENTAKKL v0.3
Taxonomic Extraction Normalization Transformation and Accounting for Kraken/bracKen fiLes

usage perl -w tentakkl.pl [options] -config minitax.cfg -bracken kraken_output/*_bracken.kreport

-config file       list of target taxa, text file, one taxon per line
                   preface taxon with '-' to have reads at that level removed. Child taxa unaffected
-bracken files     bracken-corrected kraken taxonomy reports
-kraken files      [optional] kraken taxonomy reports, used to extract unclassified reads
-out file          output filename (STDOUT by default)
-outfmt list|wide  list=tidy or wide=matrix; list has counts and normalized; wide uses normalize option
-normalize n|b|k   (outfmt=wide) n=counts
                                 b=normalize to 1 using bracken total
                                 k=normalize to 1 using kraken total (incl. unclassified)
-add_lost          add reads lost during bracken read reassignment to a root taxon
-add_unclassified  add unclassified reads category
-precision int     number of decimal places when normalizing
-logfile file      write a logfile (still under development)
-verbose int       0=no info, 1=file-level info, 2=taxa-level info

Quick Start

This is an example taxonomic configuration file

15:05 biowulf minitax$ cat minitax.config  
#hierarchical list of target taxa
#indenting is for readability only
#use a minus (-) to drop taxa (but not child taxa)

Bacteria
 Actinomycetota
  Cutibacterium acnes
  Corynebacterium tuberculostearicum
 Bacillota
  Staphylococcus aureus
  Staphylococcus capitis
  Staphylococcus epidermidis
  Staphylococcus hominis
 Pseudomonadota
 Bacteroidota
Eukaryota
 Fungi
  Malassezia globosa
  Malassezia restricta
  [Candida] auris
  Homo sapiens
Archaea
Viruses
 Human papillomavirus
 Merkel cell polyomavirus

You might run tentakkl on a collection of bracken files like:

15:22 biowulf minitax$ perl -w tentakkl.pl -bracken kraken_output/*_bracken_species.kreport -kraken kraken_output/Met????.kreport -verbose 1 -config minitax.config -add_lost -add_unclassified -outfmt list > test5.txt

That list format file can be visualized in R