Merge https://github.com/terrimporter/CO1Classifier

README.md

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+# Introduction
+
+This repository contains training sets that can be used with the Ribosomal Database Project classifier (Wang et al., 2007) to taxonomically assign Eukaryote CO1 mtDNA sequences.
+
+# How to cite
+
+If you use these training sets in a publication, please cite:
+
+## Training set 
+Porter, T.M., & Hajibabaei, M. (2018) Automated high throughput animal CO1 metabarcode classification.  Scientific Reports, 8, 4226.
+
+## Classifier 
+Wang et al. (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.  Applied and Environmental Microbiology, 73: 5261.
+
+# Releases
+
+December 4, 2017 - 
+
+The latest release can be downloaded from here:
+https://github.com/terrimporter/CO1Classifier/releases/tag/v2.0
+The CO1v2_trained.tar.gz file should be decompressed and used directly with the RDP Classifier to make taxonomic assignments to the species rank.
+
+The reference files for the latest release can be downloaded from here:
+https://github.com/terrimporter/CO1Classifier/releases/tag/v2.0-ref
+The CO1v2_training.tar.gz file should be decompressed.  The folder contains the original taxonomy and fasta files that are included here for reference only.  They were originally mined from GenBank in August 2016.
+
+The original release described in Porter & Hajibabaei (2017) can be downloaded from here:
+https://github.com/terrimporter/CO1Classifier/releases/tag/v1.0
+The CO1v1_trained.tar.gz file should be decompressed and used directly with the RDP Classifier to make taxonomic assignments to the genus rank.
+
+The reference files for the original release described in Porter & Hajibabaei (2017) can be downloaded from here:
+https://github.com/terrimporter/CO1Classifier/releases/tag/v1.0-ref
+The CO1v1_training.tar.gz file should be decompressed.  The folder contains the original taxonomy and fasta files that are included here for reference only.  They were originally mined from GenBank in August 2016.
+
+# How to use
+
+Decompress the tar.gz file:
+
+$ tar -xvzf FileName.tar.gz
+
+Use with the RDP classifier:
+
+java -Xmx8g -jar /path/to/rdp_classifier_2.12/dist/classifier.jar classify -t /path/to/CO1version_trained/rRNAClassifier.properties -o ClassifiedQueryFilename QueryFilename
+
+# Additional information
+
+For additional information on choosing appropriate bootstrap support cutoff values, see Porter & Hajibabaei (2017):
+https://doi.org/10.1101/219675
+
+For additional information on how to run the RDP classifier, see the RDPclassifier 2.12 README.
+
+The RDP classifier v2.12 can be downloaded from:
+https://sourceforge.net/projects/rdp-classifier/
+
+# Acknowledgements
+
+We acknowledge support from the Canadian federal Genomics R & D Initiative interdepartmental EcoBiomics project.