hitac 2.0.14

Hierarchical taxonomic classifier.

HiTaC

HiTaC is an open-source hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME 2.

Quick links

• Benchmark

Benchmark

HiTaC was thoroughly evaluated with the TAXXI benchmark, consistently achieving higher accuracy and sensitivity as evidenced in the figures below.

For reproducibility, a Snakemake pipeline was created. Instructions on how to run it and source code are available at https://gitlab.com/dacs-hpi/hitac/-/tree/master/benchmark.

Installation

HiTaC dependends on QIIME 2. We recommend using QIIME 2 version 2021.8. To install QIIME 2 in a new conda environment and activate it, please run:

wget https://data.qiime2.org/distro/core/qiime2-2021.8-py38-linux-conda.yml
conda env create -n qiime2-2021.8 --file qiime2-2021.8-py38-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2021.8-py38-linux-conda.yml
conda activate qiime2-2020.2

Afterwards, HiTaC can also be installed with conda:

conda install -c conda-forge -c bioconda hitac

For conda installation instructions, we refer the reader to https://conda.io/projects/conda/en/latest/user-guide/install/index.html.

Alternatively, HiTaC can be installed with pip in an environment where QIIME 2 was previously installed:

pip install hitac

Lastly, HiTaC and all its dependencies can be download as a docker image:

docker pull mirand863/hitac:latest

The downloaded image can then be started with:

docker run -it mirand863/hitac:latest /bin/bash

Running

For an interactive tutorial, we refer the reader to our Google Colabs notebook.

To see the usage run qiime hitac --help or qiime hitac [command] --help if you want further help with a specific command.

Usage: qiime hitac [OPTIONS] COMMAND [ARGS]...

  Description: This QIIME 2 plugin wraps HiTaC for hierarchical taxonomic
  classification.

  Plugin website: https://gitlab.com/dacs-hpi/hitac

  Getting user support: Please post to the QIIME 2 forum for help with this
  plugin: https://forum.qiime2.org

Options:
  --version    Show the version and exit.
  --citations  Show citations and exit.
  --help       Show this message and exit.

Commands:
  classify    Hierarchical classification with HiTaC's pre-fitted model
  filter      Hierarchical classification filtering with HiTaC's pre-fitted
              model

  fit         Train HiTaC's hierarchical classifier
  fit-filter  Train HiTaC's hierarchical filter

Input Files

HiTaC accepts taxonomy in TSV format and training and test files in FASTA format. All these files must be previously imported by QIIME 2. For example:

qiime tools import \
--input-path $qfa \
--output-path q-seqs.qza \
--type 'FeatureData[Sequence]'

qiime tools import \
--input-path dbq.fa \
--output-path db-seqs.qza \
--type 'FeatureData[Sequence]'

qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-format HeaderlessTSVTaxonomyFormat \
--input-path db-tax.txt \
--output-path db-tax.qza

Training and predicting taxonomies

To train the model and classify, simply run:

qiime hitac fit \
--i-reference-reads db-seqs.qza \
--i-reference-taxonomy db-tax.qza \
--o-classifier classifier.qza

qiime hitac classify \
--i-classifier classifier.qza \
--i-reads q-seqs.qza \
--o-classification classifier_output.qza

Additionally, a filter can be trained to remove ranks where the predictions might be inaccurate and to compute the confidence score:

qiime hitac fit-filter \
--i-reference-reads db-seqs.qza \
--i-reference-taxonomy db-tax.qza \
--o-filter filter.qza

qiime hitac filter \
--i-filter filter.qza \
--i-reads q-seqs.qza \
--i-classification classifier_output.qza \
--o-filtered-classification filter_output.qza

Output File

The predictions can be exported from QIIME 2 to a TSV file:

qiime tools export \
--input-path classifier_output.qza \
--output-path output_dir

or alternativelly if the filter was used:

qiime tools export \
--input-path filter_output.qza \
--output-path output_dir

The first column in the TSV file contains the identifier of the test sequence and the second column holds the predictions made by HiTaC. For example:

Feature ID	Taxon	Confidence
EU254776;tax=d:Fungi,p:Ascomycota,c:Sordariomycetes,o:Diaporthales,f:Gnomoniaceae,g:Gnomonia;	d__Fungi; p__Ascomycota; c__Sordariomycetes; o__Diaporthales; f__Valsaceae; g__Cryptosporella	-1
FJ711636;tax=d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Agaricales,f:Marasmiaceae,g:Armillaria;	d__Fungi; p__Basidiomycota; c__Agaricomycetes; o__Agaricales; f__Marasmiaceae; g__Armillaria	-1
UDB016040;tax=d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Russulales,f:Russulaceae,g:Russula;	d__Fungi; p__Basidiomycota; c__Agaricomycetes; o__Russulales; f__Russulaceae; g__Russula	-1
GU827310;tax=d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Ramalinaceae,g:Ramalina;	d__Fungi; p__Ascomycota; c__Lecanoromycetes; o__Lecanorales; f__Ramalinaceae; g__Ramalina	-1
JN943699;tax=d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Parmeliaceae,g:Melanohalea;	d__Fungi; p__Ascomycota; c__Lecanoromycetes; o__Lecanorales; f__Parmeliaceae; g__Punctelia	-1

Citation

If you use HiTaC, please cite:

Miranda, Fábio M., et al. "HiTaC: Hierarchical Taxonomic Classification of Fungal ITS Sequences." bioRxiv (2020).

@article{miranda2020hitac,
  title={HiTaC: Hierarchical Taxonomic Classification of Fungal ITS Sequences},
  author={Miranda, F{\'a}bio M and Azevedo, Vasco AC and Renard, Bernhard Y and Piro, Vitor C and Ramos, Rommel TJ},
  journal={bioRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory}
}