From ffa784f911bf3add75839a382e393972e0cc1263 Mon Sep 17 00:00:00 2001
From: "Teresita M. Porter" <terrimporter@gmail.com>
Date: Wed, 31 Mar 2021 16:35:07 -0400
Subject: [PATCH] Update README.md

---
 README.md | 36 ++++++++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 5bc9f45..d12ef60 100644
--- a/README.md
+++ b/README.md
@@ -18,15 +18,31 @@ If you use this reference set with the RDP classifier please also cite the naive
 
 Wang et al. (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73: 5261.
 
-## 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/mydata_trained/rRNAClassifier.properties -o ClassifiedQueryFilename QueryFilename
+## Quick Start
+```linux
+############ Install the RDP classifier if you need it
+# The easiest way to install the RDP classifier v2.13 is using conda
+conda install -c bioconda rdp_classifier
+# Alternatively, you can install from SourceForge and run with java if you don't use conda
+wget https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.13.zip
+# decompress it
+unzip rdp_classifier_2.13
+# record path to classifier.jar ex. /path/to/rdp_classifier_2.13/dist/classifier.jar
+
+############ Get the latest 12S training set
+wget https://github.com/terrimporter/12SfishClassifier/releases/download/v1.0/mydata_trained.tar.gz
+
+# decompress it
+tar -xvf mydata_trained.tar.gz
+
+# record the path to the rRNAClassifier.properties file ex. /path/to/mydata_trained/rRNAClassifier.properties
+
+############ Run the RDP Classifier 
+# If it was installed using conda, run it like this:
+rdp_classifier -Xmx8g classify -t /path/to/mydata_trained/rRNAClassifier.properties -o rdp.output query.fasta
+# Otherwise run it using java like this:
+java -Xmx8g -jar /path/to/rdp_classifier_2.13/classifier.jar -t /path/to/mydata_trained/rRNAClassifie
+```
 
 # Releases
 
@@ -79,4 +95,4 @@ Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007). Naive Bayesian Cl
 
 We acknowledge support from the Canadian federal Genomics Research & Development Initiative (GRDI), Metagenomics-Based Ecosystem Biomonitoring (Ecobiomics) project.
 
-Last updated: April 3, 2020
+Last updated: March 31, 2021