The Read-based Taxonomy Classification (v1.0.1)


Workflow Overview

The pipeline takes in sequencing files (single- or paired-end) and profiles them using multiple taxonomic classification tools with the Cromwell as the workflow manager.

Workflow Availability

The workflow is available in GitHub:; the corresponding Docker image is available in DockerHub:

Requirements for Execution:

(recommendations are in bold)

  • WDL-capable Workflow Execution Tool (Cromwell)
  • Container Runtime that can load Docker images (Docker v2.1.0.3 or higher)

Hardware Requirements:

  • Disk space: 152 GB for databases (55 GB, 89 GB, and 8 GB for GOTTCHA2, Kraken2 and Centrifuge databases, respectively)
  • 60 GB RAM

Workflow Dependencies

Third party software:

(These are included in the Docker image.)

Requisite databases:

The database for each tool must be downloaded and installed. These databases total 152 GB.

  • GOTTCHA2 database (gottcha2/):

The database contains complete genomes of bacteria, archaea and viruses from RefSeq Release 90. The following commands will download the database:

tar -xvf
  • Kraken2 database (kraken2/):

This is a standard Kraken 2 database, built from NCBI RefSeq genomes. The following commands will download the database:

mkdir kraken2
tar -xzvf k2_standard_20201202.tar.gz -C kraken2
rm k2_standard_20201202.tar.gz
  • Centrifuge database (centrifuge/):

This is a compressed database built from RefSeq genomes of Bacteria and Archaea. The following commands will download the database:

mkdir centrifuge
tar -xzvf p_compressed_2018_4_15.tar.gz -C centrifuge
rm p_compressed_2018_4_15.tar.gz

Sample dataset(s):

Zymobiomics mock-community DNA control (SRR7877884); this dataset is ~7 GB.

Input: A JSON file containing the following information: 1. selection of profiling tools (set as true if selected) 2. the paths to the required database(s) for the tools selected 3. the paths to the input fastq file(s) (paired-end data is shown; this can be the output of the Reads QC workflow in interleaved format which will be treated as single-end data.) 4. the prefix for the output file names 5. the path of the output directory 6. CPU number requested for the run.

    "ReadbasedAnalysis.enabled_tools": {
        "gottcha2": true,
        "kraken2": true,
        "centrifuge": true
    "ReadbasedAnalysis.db": {
        "gottcha2": "/path/to/database/",
        "kraken2": " /path/to/kraken2",
        "centrifuge": "/path/to/centrifuge/p_compressed"
    "ReadbasedAnalysis.reads": [
    "ReadbasedAnalysis.paired": true,
    "ReadbasedAnalysis.prefix": "SRR7877884",
    "ReadbasedAnalysis.outdir": "/path/to/ReadbasedAnalysis",
    "ReadbasedAnalysis.cpu": 4


The workflow creates an output JSON file and individual output sub-directories for each tool which include tabular classification results, a tabular report, and a Krona plot (html).:

|-- SRR7877884.json
|-- centrifuge
|   |-- SRR7877884.classification.tsv
|   |--
|   `-- SRR7877884.krona.html
|-- gottcha2
|   |-- SRR7877884.full.tsv
|   |-- SRR7877884.krona.html
|   `-- SRR7877884.tsv
`-- kraken2
    |-- SRR7877884.classification.tsv
    |-- SRR7877884.krona.html

Below is an example of the output directory files with descriptions to the right.

FileName Description
SRR7877884.json ReadbasedAnalysis result JSON file
centrifuge/SRR7877884.classification.tsv Centrifuge output read classification TSV file
centrifuge/ Centrifuge output report TSV file
centrifuge/SRR7877884.krona.html Centrifuge krona plot HTML file
gottcha2/SRR7877884.full.tsv GOTTCHA2 detail output TSV file
gottcha2/SRR7877884.tsv GOTTCHA2 output report TSV file
gottcha2/SRR7877884.krona.html GOTTCHA2 krona plot HTML file
kraken2/SRR7877884.classification.tsv Kraken2 output read classification TSV file
kraken2/ Kraken2 output report TSV file
kraken2/SRR7877884.krona.html Kraken2 krona plot HTML file

Version History

1.0.1 (release date 01/14/2021; previous versions: 1.0.0)

Point of contact

Package maintainer: Po-E Li <>