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Benjamin Linard edited this page Jul 12, 2018 · 34 revisions

Welcome to the RAPPAS wiki!

You will find here tutorials describing use cases of RAPPAS as well as comments on the different analysis options it provides. All tutorials are valid for a UNIX or MAC operating system. RAPPAS can be installed on Windows systems but you will need to adapt the following commands accordingly.

Table of contents

A. Detailed Installation

B. Tutorials

C. Comments on ancestral sequence reconstruction

D. A non-exhaustive list of other software related to phylogenetic placements

Detailed installation

Prerequisites

  • RAPPAS compilation requires a clean JDK 1.8 javac compiler installation. Java >=1.8 is a compulsory requirement as some operations are based on Lambda expressions.
  • Apache Ant is used to facilitate the compilation.

Debian distributions (Debian, Ubuntu, Mint ...)

  1. If not already done, please install the OpenJDK libraries of the proprietary Oracle JDK 1.8.

Using OpenJDK 1.8:

#install packages
sudo apt-get update
sudo apt-get install openjdk-8-jdk
#update relevant symlinks to make v1.8 default
sudo update-java-alternatives --set java-1.8.0-openjdk-amd64

Using the proprietary Oracle JDK 1.8:

#install packages
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer
#update relevant symlinks to make v1.8 default
sudo apt-get install oracle-java8-set-default
  1. Install Apache Ant:
sudo apt-get install ant

If everything went fine, the command java -version should return lines similar to:

java version "1.8.0_161"          <<--- the version must be > 1.8.x
Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)
  1. Download and build RAPPAS
git clone -b master https://github.com/blinard-BIOINFO/RAPPAS.git
cd RAPPAS && ant -f build-cli.xml
  1. Test RAPPAS executable

If everything went fine, you should be able to launch RAPPAS. A simple test can be to display its help page: java -jar dist/RAPPAS.jar -h Note: java -jar XXX.jar calls the java interpreter on a jar archive. Any RAPPAS command-line option must appear after these elements.

MAC OS

  1. If not already done, install the OpenJDK libraries of the proprietary Oracle JDK 1.8. Download the JDK from the Oracle JDK 8 webpage.

  2. Unpack the jdk by running the file jdk-8uxxx-macosx-x64.dmg.

3.Your JDK is installed. Note that you may have to explicitely export the JDK with the command: export JAVA_HOME=/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home To avoid to reproduced this step, just add this line in your bash profile.

  1. If everything went fine, the command java -v should return lines similar to:
java version "1.8.0_161"          <<--- the version must be > 1.8.x
Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)
  1. Ant is bundle with the latest version of MAC OS. But if your need to install it:
#install brew if not already done
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew update
brew install ant
  1. Download and build RAPPAS
git clone -b master https://github.com/blinard-BIOINFO/RAPPAS.git
cd RAPPAS && ant -f build-cli.xml
  1. Test RAPPAS executable

If everything went fine, you should be able to launch RAPPAS. A simple test can be to display its help page: java -jar dist/RAPPAS.jar -h Note: java -jar XXX.jar calls the java interpreter on a jar archive. Any RAPPAS command-line option must appear after these elements.

Tutorials

Tutorial n°1: Accurate identification of viruses

Tutorial n°2: Diversity estimation using bacterial 16S rRNAs

This tutorial is an analogue to the tutorial provided on this page. It represents a typical case of bacterial community analysis.

  • The reference tree contains 652 bacterial taxa and is built from the alignment of their 16S rRNA genes (a classical barcode in bacterial metagenomics). It was retrieved from (link).
  • The sample is a collection of millions of real-world amplicons of 150bp (typically generated during a metabarcoding experiment). These were retrieved from the Earth Mi-crobiome Project (Thompson et al., 2017) via the European Nucleotide Archive (Silvester et al., 2018) using custom scripts from github.com/biocore/emp.

The main steps of the approach are:

  • Build a RAPPAS database from the reference tree.
  • Place 1 millions of amplicons on this reference.
  • Produce a diversity measure from the placement results.
  • Optionnally, visualize the placements in iTOL.
  1. Download and build RAPPAS, move into the tutorial directory.
git clone -b master https://github.com/blinard-BIOINFO/RAPPAS.git
cd RAPPAS && ant -f build-cli.xml
cd ../tutorials/tutorial_2
  1. Build the RAPPAS Database
java -Xmx8G -jar ../../RAPPAS/dist/RAPPAS.jar -m b -w ./ -k 8 -r refalign.fasta -t reftree.nwk -s nucl -b

Essential points:

  • The '-Xmx' option:
  • The 'w' option:
  • Impact of the '-k' parameter:
  • The '-b' option:
  1. Place the 1,000,000 amplicons of the sample
java -Xmx8G -jar ../../RAPPAS/dist/RAPPAS.jar -m p -d XXX.union -q sample.fasta

This produce a 'sample.fasta.jplace' file in the log directory

Comments on ancestral sequence reconstruction

A non-exhaustive list of software related to phylogenetic placements

Placement post-analysis

Placement visualisation

Alternatives to RAPPAS

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