metaclassifier 1.0.1

MetaClassifier is an integrated pipeline for classifying and quantifying DNA metabarcoding data into taxonomy groups

MetaClassifier

Overview

MetaClassifier is an integrated pipeline for identifying the floral composition of honey using DNA metabarcoding to determine the plants that honey bees visit. MetaClassifier utilizes a database of marker sequences and their corresponding taxonomy lineage information to classify high-throughput metabarcoding sample sequencing reads 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.

Installation

MetaClassifier requires dependencies and external tools that need to be installed and available on the environment the pipeline can be used. Not a requirement if insatalling using Bioconda.

Dependecies

• Python (version >=3.7)
• pandas (version >=1.2.2)

External tools

• 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

Python package installation

MetaClassifier is available through pypi. To install, type:

pip install metaclassifier

Repository from GitHub

Either "git clone https://github.com/ewafula/MetaClassifier.git" or download and "unzip MetaClassifier-main.zip"
cd MetaClassifier/
python setup.py install

Bioconda package

This requires a working Conda installation.

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=1.0.1

Marker reference databases

MetaCurator reference databases with taxonomy lineage information reformated to work with MetaClassifier. Detailed step by step tutorial workflow for creating reference marker database is descrribe on the GitHub MetaCurator database repository

• MetabarcodeDBs

Basic usage

metaclassifier [options] <SAMPLE_FILE> <DB_DIR> <CONFIG_FILE>

Please consult the MetaClassifier manual for a detailed description and usage of all options.

Citation

If you use MetaClassifier please cite the following paper the 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

License

MetaClassifier is distributed under the GNU GPL v3.0 For more information, see license.