Ray assembler

Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere
and is implemented using peer-to-peer communication.

Ray is implemented using RayPlatform, a message-passing-interface programming framework.

Ray is documented in

• Documentation/ (many files)
• MANUAL_PAGE.txt (command-line options, same as Ray -help)
• README.md (general)
• INSTALL.txt (quick installation)

Solutions (all bundled in a single Product called Ray)

• de novo genome assembly
• de novo meta-genome assembly (with Ray Méta)
• de novo transcriptome assembly (works, but not tested a lot)
• quantification of contig abundances
• quantification of microbiome consortia members (with Ray Communities)
• quantification of transcript expression
• taxonomy profiling of samples (with Ray Communities)
• gene ontology profiling of samples (with Ray Ontologies)

see Documentation/BiologicalAbundances.txt

Website

• http://denovoassembler.sf.net

Code repositories

• http://github.com/sebhtml/ray (Ray plugins for genomics)

• http://github.com/sebhtml/RayPlatform (the engine RayPlatform)

If you want to contribute, clone the repository, make changes
and I (Sébastien Boisvert) will pull from you after reviewing
the code changes.

Other related repositories

• http://github.com/sebhtml/Ray-TestSuite (system tests & unit tests)

• http://github.com/sebhtml/Ray.web (Ray SourceForge web site)

• http://github.com/sebhtml/ray-logo (artworks)

Mailing lists

• Users: denovoassembler-users AT lists.sourceforge.net

• Read it on gmane: http://blog.gmane.org/gmane.science.biology.ray-genome-assembler

• Development/hacking: denovoassembler-devel AT lists.sourceforge.net

• SEQanswers: http://seqanswers.com/forums/showthread.php?t=4301

Installation

You need a C++ compiler (supporting C++ 1998), make, an implementation of MPI (supporting MPI 2.2).

Compilation

tar xjf Ray-x.y.z.tar.bz2
cd Ray-x.y.z
make PREFIX=build
make install
ls build

Compilation using CMake

tar xjf Ray-x.y.z.tar.bz2
cd Ray-x.y.z
mkdir build
cd build
cmake ..
make

Change the compiler

make PREFIX=build2000 MPICXX=/software/openmpi-1.4.3/bin/mpicxx
make install

Tested C++ compilers: see Documentation/COMPILERS.txt

Faster execution

Some processors have the popcnt instruction and other cool instructions.
With gcc, add -march=native to build Ray for the processor used for
the compilation.

make PREFIX=Build.native DEBUG=n ASSERT=n EXTRA=" -march=native"
make install

The best way to build Ray is to use whole-program optimization.
With gcc, use this script:

./scripts/Build-Link-Time-Optimization.sh

Use large k-mers

make PREFIX=Ray-Large-k-mers MAXKMERLENGTH=64
# wait
make install
mpirun -np 512 Ray-Large-k-mers/Ray -k 63 -p lib1_1.fastq lib1_2.fastq \
-p lib2_1.fastq lib2_2.fastq -o DeadlyBug,Assembler=Ray,K=63
# wait
ls DeadlyBug,Assembler=Ray,K=63/Scaffolds.fasta

Compilation options

make PREFIX=build-3000 MAXKMERLENGTH=64 HAVE_LIBZ=y HAVE_LIBBZ2=y \
ASSERT=n FORCE_PACKING=y
# wait
make install
ls build-3000

see the Makefile for more.

Run Ray

To run Ray on paired reads:

mpiexec -n 25 Ray -k31 -p lib1.left.fasta lib1.right.fasta -p lib2.left.fasta lib2.right.fasta -o RayOutput
ls RayOutput/Contigs.fasta
ls RayOutput/Scaffolds.fasta
ls RayOutput/

Using a configuration file

Ray can be run with a configuration file instead.

mpiexec -n 16 Ray Ray.conf

Content of Ray.conf:

-k 31 # this is a comment
-p
lib1.left.fasta
lib1.right.fasta

-p
lib2.left.fasta
lib2.right.fasta

-o RayOutput

Outputted files

RayOutput/Contigs.fasta and RayOutput/Scaffolds.fasta

type Ray -help for a full list of options and outputs

Color space

Ray assembles color-space reads and generate color-space contigs.
Files must have the .csfasta extension. Nucleotide reads can not be mixed
with color-space reads. This is an experimental feature.

Publications

http://denovoassembler.sf.net/publications.html

Code

Code documentation

cd code
doxygen DoxygenConfigurationFile
cd DoxygenDocumentation/html
firefox index.html

Useful links

Cloud computing

• http://aws.amazon.com/ec2/hpc-applications/
• https://cloud.genomics.cn/
• http://szdaily.sznews.com/html/2011-08/04/content_1689998.htm
• http://www.nature.com/nbt/journal/v28/n7/full/nbt0710-691.html

Message-passing interface

• http://dskernel.blogspot.com/2011/07/understand-main-loop-of-message-passing.html
• http://cw.squyres.com/
• http://blogs.cisco.com/performance/
• http://www.parawiki.org/index.php/Message_Passing_Interface#Peer_to_Peer_Communication

Funding

Doctoral Award to S.B., Canadian Institutes of Health Research (CIHR)

Authors

see AUTHORS

Compile Ray on Microsoft Windows with Microsoft Visual Studio

see Documentation/VISUAL_STUDIO.txt