Ray statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Ray
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Tool usage distribution map

This map represents all the scientific publications referring to Ray per scientific context
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Associated diseases

This word cloud represents Ray usage per disease context
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Popular tool citations

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Protocols

Ray specifications

Information


Unique identifier OMICS_00027
Name Ray
Alternative names OCLRay, Ray Surveyor, Ray Meta
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MPI
Computer skills Advanced
Version 2.3.1
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Sebastien Boisvert
  • person_outline Jacques Corbeil

Additional information


An algorithm of Ray in OpenCL, OCLRay, is also available : http://doi.ieeecomputersociety.org/10.1109/TCBB.2017.2696522

Publications for Ray

Ray citations

 (6)
library_books

Phenetic Comparison of Prokaryotic Genomes Using k mers

2017
Mol Biol Evol
PMCID: 5850840
PMID: 28957508
DOI: 10.1093/molbev/msx200

[…] es, plasmids, bacteriophages and biosynthetic gene clusters (BGC) and observed their relationship with genome population structure for different bacterial species. This approach is implemented in the Ray Surveyor software, which is built on top of the scalable Ray framework (, ). The defining feature of Ray Surveyor is the ability to compare whole genomes based on their complete set of k-mers alon […]

call_split

Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae)

2017
Genome Announc
PMCID: 5270694
PMID: 28126935
DOI: 10.1128/genomeA.01485-16
call_split See protocol

[…] SISPA-RACE adapter sequences were trimmed from the sequencing reads using Cutadapt version 1.2.1 (), quality filtering was conducted with Prinseq-lite (), and reads were assembled into contigs using Ray Meta with a k-mer length of 25 (). Resultant contigs were aligned to the National Center for Biotechnology Information (NCBI) sequence database using BLAST. Reads were aligned back to the assemble […]

library_books

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

2016
PMCID: 5034103
PMID: 27530749
DOI: 10.1038/emi.2016.90

[…] ared from both RNA and DNA. Altogether we generated more than 2.2 billion paired-end HiSeq reads and over 32 million paired-end MiSeq reads, from which >15.8 million contigs were generated, using the Ray Meta assembler.The contigs were aligned to genomes in a custom database identifying 2524 contigs mapping to known viruses from eukaryotic hosts and ~875 000 contigs with similarity to other specie […]

library_books

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production scale biogas plants

2016
Biotechnol Biofuels
PMCID: 4960831
PMID: 27462367
DOI: 10.1186/s13068-016-0565-3

[…] genome binning, all sequencing data was combined after quality control (JGI QC pipeline: sequencing artefact removal, removal of reads containing ambiguous (N) bases and filtering based on quality). Ray Meta (v2.3.0) [] was used for assembly of the pooled sequencing data of all samples, using a k-mer size of 31. To estimate the inclusivity of our metagenome assembly, all sequencing reads were ali […]

library_books

Vancomycin gene selection in the microbiome of urban Rattus norvegicus from hospital environment

2016
PMCID: 4972940
PMID: 27412864
DOI: 10.1093/emph/eow021

[…] stance measure.To identify genes shared among sample locations, a gene was considered present in a location if at least one read mapped to the gene sequence. Assembly of the reads was performed using Ray Meta (v2.2.0 default settings) [] and contigs were mapped to the ARG-ANNOT database using bowtie2 and the contigs with a match were aligned using BLASTn (v2.2.29+ default settings) to verify their […]

library_books

Social networks predict gut microbiome composition in wild baboons

2015
eLife
PMCID: 4379495
PMID: 25774601
DOI: 10.7554/eLife.05224.023

[…] ing the complete set of 1.4 billion raw reads. This approach allowed us to evaluate whether our results were robust to our methods for estimating species abundance. Reads were assembled de novo using Ray Meta, a short read de Bruijn assembler specifically devised for metagenome data, following the authors' recommendations (). Bacterial proportions for each sample were then estimated using Ray Comm […]


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Ray institution(s)
Centre de Recherche en Infectiologie, CHU de Quebec-Universite Laval, Quebec City, QC, Canada; Centre de Recherche en Donnees Massives de l’Universite Laval, Quebec City, QC, Canada; Departement de Medecine Moleculaire, Universite Laval, Quebec City, QC, Canada; Gydle Inc., Quebec City, QC, Canada; Departement de Biochimie, Microbiologie et Bio-informatique, Universite Laval, Quebec City, QC, Canada; Departement d’Informatique et de Genie Logiciel, Universite Laval, Quebec City, QC, Canada
Ray funding source(s)
Supported by a Mitacs post-doctoral fellowship, the Fonds de recherche du Quebec-Sante, the Canada Foundation for Innovation (CFI), the National Science and Engineering Research Council (NSERC), NanoQue´bec, and the Fonds Que´be´cois de Recherche sur la Nature et les Technologies (FQRNT).

Ray review

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Fabien Pichon

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Desktop
A light and efficient assembler that perform well for small genomes (not tried on eucaryote ones), with good computer memory gestion (the only one that didn't crash because of a segmentation fault!).