Metagenomics Practical

Metagenomics assemblies with Ray

Ray is a particularly interesting genome assembler due to several unusual features:

• It can scale to arbitrary numbers of processors and machines by distributing its assembly graph
• It has several functions specific to metagenome assembly ‘Ray Meta’
• Ray’s author, @sebhtml is incredibly responsive on Twitter :)
• Ray will happily mix input from several different sequencing techniques, e.g. Illumina and 454
• If run with the write-kmers option enabled, the resulting assembly graph may be viewed using the separate Ray Cloud Browser software

Installing Ray

Dependencies

sudo apt-get install build-essential
sudo apt-get install git
sudo apt-get install openmpi1.6-bin openmpi1.6-common libopenmpi1.6-dev

Installing Ray from source code

git clone https://github.com/sebhtml/ray
git clone https://github.com/sebhtml/RayPlatform

cd ray
HAVE_LIBZ=y MAXKMERLENGTH=64 make

You can add this to your PATH:

export PATH=$PATH:`pwd`

A simple command-line for multi-processor execution:

For paired-end reads:

mpirun -np 8 Ray -k 31 -p pair1.fastq.gz pair2.fastq.gz -o output_directory

For interleaved paired-end reads:

mpirun -np 8 Ray -k 31 -i pairs.fastq.gz -o output_directory

For single-end reads:

mpirun -np 8 Ray -k 31 -s reads.fastq.gz -o output_directory

If you want to run Ray Cloud Browser, you will want the -write-kmers option:

mpirun -np 8 Ray -write-kmers -k 31 -p pair1.fastq.gz pair2.fastq.gz -o output directory

If you run via a cluster, i.e. StarCluster, mpirun can be set to execute on multiple machines, e.g.:

mpirun -np 8 -H host1,host2,host3,host4 -k 31 -p pair1.fastq.gz pair2.fastq.gz -o x

For more command-line options, see:

https://github.com/sebhtml/ray/blob/master/MANUAL_PAGE.txt

Ray Cloud Browser

Here is a useful script to set up Ray Cloud Browser from a kmers.txt and Contigs.fasta file:

#!/bin/bash
tag=$1
kmerfile=$2
contigfile=$3
mapid=$4
sectionid=$5

RayCloudBrowser-client create-map $kmerfile $tag.dat
RayCloudBrowser-client add-map config.json "$tag" $tag.dat
RayCloudBrowser-client create-section $contigfile $tag-contigs.dat
RayCloudBrowser-client create-map-annotations-with-section $tag.dat $tag-contigs.dat $sectionid
RayCloudBrowser-client add-section config.json $mapid "$tag Contigs" $tag-contigs.dat