Ray -- Parallel genome assemblies for parallel DNA sequencing

README.md

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 free software distributed under the terms of the GNU General Public License, version 3 (GPLv3).

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)

Standard:

Metagenomics:

  • Ray Meta: de novo metagenome assembly (works by default) => http://genomebiology.com/2012/13/12/R122
  • Ray Communities: quantification of microbiome consortia members (with Ray Communities with -search) => Documentation/BiologicalAbundances.txt
  • Ray Communities: taxonomy profiling of samples (with -search and -with-taxonomy) => Documentation/Taxonomy.txt
  • Ray Ontology: gene ontology profiling of samples (with -search and -gene-ontology) => Documentation/GeneOntology.txt
  • Ray Surveyor: compare genomic content between samples (with -run-surveyor) => Documentation/Ray-Surveyor.md

Transcriptomics:

  • de novo transcriptome assembly (works, but not tested a lot)
  • quantification of transcript expression

Distributors

In progress:

Website

Code repositories

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

Mailing lists

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

Parallel I/O

To compile with MPI I/O, use this:

make MPI_IO=y

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

Another 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

Message-passing interface

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