MetaClassifier is an integrated pipeline for identifying the plant taxonomic composition of DNA from pollen baskets or honey, using DNA metabarcoding to determine the source plant species composition. MetaClassifier uses a database of marker sequences and their corresponding taxonomic lineage information to classify high-throughput metabarcoding sequence read data into taxonomic groups and quantify taxon abundance.MetaClassifier can also be employed in other studies that utilize barcoding, metabarcoding, and metagenomics techniques to characterize richness, abundance, relatedness, and interactions in ecological communities.
In addition to this README file, you can consult the MetaClassifier manual for more detailed information.
MetaClassifier requires dependencies and external tools that need to be installed and available on the environment where the pipeline will be used. This is not a requirement if installing MetaClassifier in Bioconda.
- PEAR for merging overlapping paired-end (PE) reads
- seqtk for converting FASTQ to FASTA sequence format
- VSEARCH for searching searching high-throughtput sequence read data against marker database
MetaClassifier is available through pypi. To install, type:
pip install metaclassifier
Either "git clone https://github.com/ewafula/MetaClassifier.git" or download and "unzip MetaClassifier-main.zip"
cd MetaClassifier/
python setup.py install
This requires a working Conda installation. A MetaClassifier docker container is also available on the Bioconda.
conda install -c bioconda metaclassifier
We recommend installing MetaClassifier in a new separate environment from the base for all dependencies to be properly resolved by conda. To install, type:
conda create -n "metaclassifier" -c bioconda metaclassifier
MetaCurator reference databases with taxonomic lineage information reformatted to work with MetaClassifier. Detailed step by step tutorial workflow for creating reference marker database is described on the GitHub MetaCurator database repository
metaclassifier [options] <SAMPLE_FILE> <DB_DIR> <CONFIG_FILE>
Please consult the MetaClassifier manual for a detailed description and usage of all options.
If you use MetaClassifier please cite the following paper that describes the methodology:
Characterizing the floral resources of a North American metropolis using a honey bee foraging assay.
Douglas B. Sponsler, Don Shump, Rodney T. Richardson, Christina M. Grozinger.
Ecosphere 11, no. 4 (2020): e03102.
DOI: https://doi.org/10.1002/ecs2.3102
MetaClassifier is distributed under the GNU GPL v3.0 -for more information, see license.