Hierarchical taxonomic classifier.
Project description
HiTaC
HiTaC is an open-source hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME 2.
Quick links
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.
Install
Option 1: Conda
HiTaC dependends on QIIME 2. We recommend using QIIME 2 version 2022.2. To install QIIME 2 in a GNU/Linux machine, run:
wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml
conda env create -n hitac --file qiime2-2022.2-py38-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2022.2-py38-linux-conda.yml
Note: Instructions on how to install on Windows and macOS are available at QIIME 2 docs.
Afterwards, the new conda environment created in the last step can be activated and HiTaC can be installed:
conda activate hitac
conda install -c conda-forge -c bioconda hitac
For conda installation instructions, we refer the reader to Conda's user guide.
Option 2: Pip
Alternatively, HiTaC can be installed with pip in an environment where QIIME 2 was previously installed:
pip install hitac
Option 3: Docker
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
Quick start
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
Support
If you run into any problems or issues, please create a GitLab issue and we will try our best to help.
We strive to provide good support through our issue tracker on GitLab. However, if you'd like to receive private support with:
- Phone / video calls to discuss your specific use case and get recommendations
- Private discussions over Slack or Mattermost
Please reach out to fabio.malchermiranda@hpi.de.
Contributing
We are a small team on a mission to improve ITS taxonomic classification, and we will take all the help we can get! If you would like to get involved, here is information on contribution guidelines and how to test the code locally.
You can contribute in multiple ways, e.g., reporting bugs, writing or translating documentation, reviewing or refactoring code, requesting or implementing new features, etc.
Getting the latest updates
If you'd like to get updates when we release new versions, please click on the "Watch" button on the top and select "Releases only". GitLab will then send you notifications along with a changelog with each new release.
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}
}
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