.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
.TH RAY "1" "November 2012" "Ray version 2.1.0" "User Commands"
.SH NAME
Ray \- assemble genomes in parallel using the message-passing interface
.SH SYNOPSIS
.B
mpiexec
\fB\-n\fR NUMBER_OF_RANKS Ray \fB\-k\fR KMERLENGTH \fB\-p\fR l1_1.fastq l1_2.fastq \fB\-p\fR l2_1.fastq l2_2.fastq \fB\-o\fR test
.PP
.B
mpiexec
\fB\-n\fR NUMBER_OF_RANKS Ray Ray.conf # with commands in a file
.PP
.SH DESCRIPTION:
The Ray genome assembler is built on top of the RayPlatform, a generic plugin\-based
distributed and parallel compute engine that uses the message\-passing interface
for passing messages.
.PP
Ray targets several applications:
.IP
\- de novo genome assembly (with Ray vanilla)
\- de novo meta\-genome assembly (with Ray Meta)
\- 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)
.HP
\fB\-help\fR
.IP
Displays this help page.
.HP
\fB\-version\fR
.IP
Displays Ray version and compilation options.
.IP
Using a configuration file
.IP
Ray can be launched with
mpiexec \fB\-n\fR 16 Ray Ray.conf
The configuration file can include comments (starting with #).
.IP
K\-mer length
.HP
\fB\-k\fR kmerLength
.IP
Selects the length of k\-mers. The default value is 21.
It must be odd because reverse\-complement vertices are stored together.
The maximum length is defined at compilation by MAXKMERLENGTH
Larger k\-mers utilise more memory.
.IP
Inputs
.HP
\fB\-p\fR leftSequenceFile rightSequenceFile [averageOuterDistance standardDeviation]
.IP
Provides two files containing paired\-end reads.
averageOuterDistance and standardDeviation are automatically computed if not provided.
.HP
\fB\-i\fR interleavedSequenceFile [averageOuterDistance standardDeviation]
.IP
Provides one file containing interleaved paired\-end reads.
averageOuterDistance and standardDeviation are automatically computed if not provided.
.HP
\fB\-s\fR sequenceFile
.IP
Provides a file containing single\-end reads.
.IP
Outputs
.HP
\fB\-o\fR outputDirectory
.IP
Specifies the directory for outputted files. Default is RayOutput
.IP
Assembly options (defaults work well)
.HP
\fB\-disable\-recycling\fR
.IP
Disables read recycling during the assembly
reads will be set free in 3 cases:
1. the distance did not match for a pair
2. the read has not met its mate
3. the library population indicates a wrong placement
see Constrained traversal of repeats with paired sequences.
Sebastien Boisvert, Elenie Godzaridis, Francois Laviolette & Jacques Corbeil.
First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26\-27 2011, Vancouver, BC, Canada.
.HP
\fB\-disable\-scaffolder\fR
.IP
Disables the scaffolder.
.HP
\fB\-minimum\-contig\-length\fR minimumContigLength
.IP
Changes the minimum contig length, default is 100 nucleotides
.HP
\fB\-color\-space\fR
.IP
Runs in color\-space
Needs csfasta files. Activated automatically if csfasta files are provided.
.HP
\fB\-use\-maximum\-seed\-coverage\fR maximumSeedCoverageDepth
.IP
Ignores any seed with a coverage depth above this threshold.
The default is 4294967295.
.HP
\fB\-use\-minimum\-seed\-coverage\fR minimumSeedCoverageDepth
.IP
Sets the minimum seed coverage depth.
Any path with a coverage depth lower than this will be discarded. The default is 0.
.IP
Distributed storage engine (all these values are for each MPI rank)
.HP
\fB\-bloom\-filter\-bits\fR bits
.IP
Sets the number of bits for the Bloom filter
Default is 268435456 bits, 0 bits disables the Bloom filter.
.HP
\fB\-hash\-table\-buckets\fR buckets
.IP
Sets the initial number of buckets. Must be a power of 2 !
Default value: 268435456
.HP
\fB\-hash\-table\-buckets\-per\-group\fR buckets
.IP
Sets the number of buckets per group for sparse storage
Default value: 64, Must be between >=1 and <= 64
.HP
\fB\-hash\-table\-load\-factor\-threshold\fR threshold
.IP
Sets the load factor threshold for real\-time resizing
Default value: 0.75, must be >= 0.5 and < 1
.HP
\fB\-hash\-table\-verbosity\fR
.IP
Activates verbosity for the distributed storage engine
.IP
Biological abundances
.HP
\fB\-search\fR searchDirectory
.IP
Provides a directory containing fasta files to be searched in the de Bruijn graph.
Biological abundances will be written to RayOutput/BiologicalAbundances
See Documentation/BiologicalAbundances.txt
.HP
\fB\-one\-color\-per\-file\fR
.IP
Sets one color per file instead of one per sequence.
By default, each sequence in each file has a different color.
For files with large numbers of sequences, using one single color per file may be more efficient.
.IP
Taxonomic profiling with colored de Bruijn graphs
.HP
\fB\-with\-taxonomy\fR Genome\-to\-Taxon.tsv TreeOfLife\-Edges.tsv Taxon\-Names.tsv
.IP
Provides a taxonomy.
Computes and writes detailed taxonomic profiles.
See Documentation/Taxonomy.txt for details.
.TP
\fB\-gene\-ontology\fR OntologyTerms.txt
Annotations.txt
.IP
Provides an ontology and annotations.
OntologyTerms.txt is fetched from http://geneontology.org
Annotations.txt is a 2\-column file (EMBL_CDS handle       &       gene ontology identifier)
See Documentation/GeneOntology.txt
.IP
Other outputs
.HP
\fB\-enable\-neighbourhoods\fR
.IP
Computes contig neighborhoods in the de Bruijn graph
Output file: RayOutput/NeighbourhoodRelations.txt
.HP
\fB\-amos\fR
.IP
Writes the AMOS file called RayOutput/AMOS.afg
An AMOS file contains read positions on contigs.
Can be opened with software with graphical user interface.
.HP
\fB\-write\-kmers\fR
.IP
Writes k\-mer graph to RayOutput/kmers.txt
The resulting file is not utilised by Ray.
The resulting file is very large.
.HP
\fB\-write\-read\-markers\fR
.IP
Writes read markers to disk.
.HP
\fB\-write\-seeds\fR
.IP
Writes seed DNA sequences to RayOutput/Rank<rank>.RaySeeds.fasta
.HP
\fB\-write\-extensions\fR
.IP
Writes extension DNA sequences to RayOutput/Rank<rank>.RayExtensions.fasta
.HP
\fB\-write\-contig\-paths\fR
.IP
Writes contig paths with coverage values
to RayOutput/Rank<rank>.RayContigPaths.txt
.HP
\fB\-write\-marker\-summary\fR
.IP
Writes marker statistics.
.IP
Memory usage
.HP
\fB\-show\-memory\-usage\fR
.IP
Shows memory usage. Data is fetched from /proc on GNU/Linux
Needs __linux__
.HP
\fB\-show\-memory\-allocations\fR
.IP
Shows memory allocation events
.IP
Algorithm verbosity
.HP
\fB\-show\-extension\-choice\fR
.IP
Shows the choice made (with other choices) during the extension.
.HP
\fB\-show\-ending\-context\fR
.IP
Shows the ending context of each extension.
Shows the children of the vertex where extension was too difficult.
.HP
\fB\-show\-distance\-summary\fR
.IP
Shows summary of outer distances used for an extension path.
.HP
\fB\-show\-consensus\fR
.IP
Shows the consensus when a choice is done.
.IP
Checkpointing
.HP
\fB\-write\-checkpoints\fR checkpointDirectory
.IP
Write checkpoint files
.HP
\fB\-read\-checkpoints\fR checkpointDirectory
.IP
Read checkpoint files
.HP
\fB\-read\-write\-checkpoints\fR checkpointDirectory
.IP
Read and write checkpoint files
.IP
Message routing for large number of cores
.HP
\fB\-route\-messages\fR
.IP
Enables the Ray message router. Disabled by default.
Messages will be routed accordingly so that any rank can communicate directly with only a few others.
Without \fB\-route\-messages\fR, any rank can communicate directly with any other rank.
Files generated: Routing/Connections.txt, Routing/Routes.txt and Routing/RelayEvents.txt
and Routing/Summary.txt
.HP
\fB\-connection\-type\fR type
.IP
Sets the connection type for routes.
Accepted values are debruijn, hypercube, polytope, group, random, kautz and complete. Default is debruijn.
.IP
debruijn: a full de Bruijn graph a given alphabet and diameter
hypercube: a hypercube, alphabet is {0,1} and the vertices is a power of 2
polytope: a convex regular polytope, alphabet is {0,1,...,B\-1} and the vertices is a power of B
group: silly model where one representative per group can communicate with outsiders
random: Erdos-Renyi model
kautz: a full de Kautz graph, which is a subgraph of a de Bruijn graph
complete: a full graph with all the possible connections
.IP
With the type debruijn, the number of ranks must be a power of something.
Examples: 256 = 16*16, 512=8*8*8, 49=7*7, and so on.
Otherwise, don't use debruijn routing but use another one
With the type kautz, the number of ranks n must be n=(k+1)*k^(d\-1) for some k and d
.HP
\fB\-routing\-graph\-degree\fR degree
.IP
Specifies the outgoing degree for the routing graph.
See Documentation/Routing.txt
.IP
Hardware testing
.HP
\fB\-test\-network\-only\fR
.IP
Tests the network and returns.
.HP
\fB\-write\-network\-test\-raw\-data\fR
.IP
Writes one additional file per rank detailing the network test.
.HP
\fB\-exchanges\fR NumberOfExchanges
.IP
Sets the number of exchanges
.HP
\fB\-disable\-network\-test\fR
.IP
Skips the network test.
.IP
Debugging
.HP
\fB\-verify\-message\-integrity\fR
.IP
Checks message data reliability for any non\-empty message.
add '\-D CONFIG_SSE_4_2' in the Makefile to use hardware instruction (SSE 4.2)
.HP
\fB\-run\-profiler\fR
.IP
Runs the profiler as the code runs. By default, only show granularity warnings.
Running the profiler increases running times.
.HP
\fB\-with\-profiler\-details\fR
.IP
Shows number of messages sent and received in each methods during in each time slices (epochs). Needs \fB\-run\-profiler\fR.
.HP
\fB\-show\-communication\-events\fR
.IP
Shows all messages sent and received.
.HP
\fB\-show\-read\-placement\fR
.IP
Shows read placement in the graph during the extension.
.HP
\fB\-debug\-bubbles\fR
.IP
Debugs bubble code.
Bubbles can be due to heterozygous sites or sequencing errors or other (unknown) events
.HP
\fB\-debug\-seeds\fR
.IP
Debugs seed code.
Seeds are paths in the graph that are likely unique.
.HP
\fB\-debug\-fusions\fR
.IP
Debugs fusion code.
.HP
\fB\-debug\-scaffolder\fR
.IP
Debug the scaffolder.
.PP
FILES
.IP
Input files
.IP
Note: file format is determined with file extension.
.IP
\&.fasta
\&.fasta.gz (needs HAVE_LIBZ=y at compilation)
\&.fasta.bz2 (needs HAVE_LIBBZ2=y at compilation)
\&.fastq
\&.fastq.gz (needs HAVE_LIBZ=y at compilation)
\&.fastq.bz2 (needs HAVE_LIBBZ2=y at compilation)
\&.sff (paired reads must be extracted manually)
\&.csfasta (color\-space reads)
.IP
Outputted files
.IP
Scaffolds
.IP
RayOutput/Scaffolds.fasta
.IP
The scaffold sequences in FASTA format
.IP
RayOutput/ScaffoldComponents.txt
.IP
The components of each scaffold
.IP
RayOutput/ScaffoldLengths.txt
.IP
The length of each scaffold
.IP
RayOutput/ScaffoldLinks.txt
.IP
Scaffold links
.IP
Contigs
.IP
RayOutput/Contigs.fasta
.IP
Contiguous sequences in FASTA format
.IP
RayOutput/ContigLengths.txt
.IP
The lengths of contiguous sequences
.IP
Summary
.IP
RayOutput/OutputNumbers.txt
.IP
Overall numbers for the assembly
.IP
de Bruijn graph
.IP
RayOutput/CoverageDistribution.txt
.IP
The distribution of coverage values
.IP
RayOutput/CoverageDistributionAnalysis.txt
.IP
Analysis of the coverage distribution
.IP
RayOutput/degreeDistribution.txt
.IP
Distribution of ingoing and outgoing degrees
.IP
RayOutput/kmers.txt
.IP
k\-mer graph, required option: \fB\-write\-kmers\fR
.IP
The resulting file is not utilised by Ray.
The resulting file is very large.
.IP
Assembly steps
.IP
RayOutput/SeedLengthDistribution.txt
.IP
Distribution of seed length
.IP
RayOutput/Rank<rank>.OptimalReadMarkers.txt
.IP
Read markers.
.IP
RayOutput/Rank<rank>.RaySeeds.fasta
.IP
Seed DNA sequences, required option: \fB\-write\-seeds\fR
.IP
RayOutput/Rank<rank>.RayExtensions.fasta
.IP
Extension DNA sequences, required option: \fB\-write\-extensions\fR
.IP
RayOutput/Rank<rank>.RayContigPaths.txt
.IP
Contig paths with coverage values, required option: \fB\-write\-contig\-paths\fR
.IP
Paired reads
.IP
RayOutput/LibraryStatistics.txt
.IP
Estimation of outer distances for paired reads
.IP
RayOutput/Library<LibraryNumber>.txt
.IP
Frequencies for observed outer distances (insert size + read lengths)
.IP
Partition
.IP
RayOutput/NumberOfSequences.txt
.IP
Number of reads in each file
.IP
RayOutput/SequencePartition.txt
.IP
Sequence partition
.IP
Ray software
.IP
RayOutput/RayVersion.txt
.IP
The version of Ray
.IP
RayOutput/RayCommand.txt
.IP
The exact same command provided
.IP
AMOS
.IP
RayOutput/AMOS.afg
.IP
Assembly representation in AMOS format, required option: \fB\-amos\fR
.IP
Communication
.IP
RayOutput/MessagePassingInterface.txt
.IP
Number of messages sent
.IP
RayOutput/NetworkTest.txt
.IP
Latencies in microseconds
.IP
RayOutput/Rank<rank>NetworkTestData.txt
.IP
Network test raw data
.PP
DOCUMENTATION
.IP
\- mpiexec \fB\-n\fR 1 Ray \fB\-help\fR|less (always up\-to\-date)
\- This help page (always up\-to\-date)
\- The directory Documentation/
\- Manual (Portable Document Format): InstructionManual.tex (in Documentation)
\- Mailing list archives: http://sourceforge.net/mailarchive/forum.php?forum_name=denovoassembler\-users
.PP
AUTHOR
.IP
Written by Sebastien Boisvert.
.PP
REPORTING BUGS
.IP
Report bugs to denovoassembler\-users@lists.sourceforge.net
Home page: <http://denovoassembler.sourceforge.net/>
.PP
COPYRIGHT
.IP
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
.IP
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
.IP
You have received a copy of the GNU General Public License
along with this program (see LICENSE).
.PP
Ray 2.1.0
.PP
License for Ray: GNU General Public License version 3
RayPlatform version: 1.1.0
License for RayPlatform: GNU Lesser General Public License version 3
.PP
MAXKMERLENGTH: 32
KMER_U64_ARRAY_SIZE: 1
Maximum coverage depth stored by CoverageDepth: 4294967295
MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = y
HAVE_LIBBZ2 = y
CONFIG_PROFILER_COLLECT = n
CONFIG_CLOCK_GETTIME = n
__linux__ = y
_MSC_VER = n
__GNUC__ = y
RAY_32_BITS = n
RAY_64_BITS = y
MPI standard version: MPI 2.1
MPI library: Open\-MPI 1.4.2
Compiler: GNU gcc/g++ 4.4.5