From 777492920fe964b29c074d9e62e14a4fa0136c90 Mon Sep 17 00:00:00 2001
From: "Teresita M. Porter" <terrimporter@gmail.com>
Date: Wed, 31 Mar 2021 16:31:52 -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 9cc4b03..4de948d 100644
--- a/README.md
+++ b/README.md
@@ -14,15 +14,31 @@ If you use this reference set with the RDP classifier please also cite:
 
 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 18S training set
+wget https://github.com/terrimporter/18SClassifier/releases/download/v4.1/18Sv4.1_mydata_trained.zip
+
+# decompress it
+unzip 18Sv4.1_mydata_trained.zip
+
+# 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/rRNAClassifier.properties -o rdp.output query.fasta
+```
 
 # Releases
 
@@ -223,4 +239,4 @@ Yilmaz, P., Parfrey, L.W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., et al.
 
 We acknowledge support from the Canadian federal Genomics Research & Development Initiative (GRDI), Metagenomics-Based Ecosystem Biomonitoring (Ecobiomics) project.
 
-Last updated: August 18, 2020
+Last updated: March 31, 2021