Ray is a particularly interesting genome assembler due to several unusual features:
sudo apt-get install build-essential
sudo apt-get install git
sudo apt-get install openmpi1.6-bin openmpi1.6-common libopenmpi1.6-dev
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:
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
Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.
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