--- /dev/null 2012-11-27 10:10:35.990752806 -0500
+++ Ray.1 2012-11-29 21:48:32.447898203 -0500
@@ -0,0 +1,407 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.12.
+.TH RAY "1" "November 2012" "Ray 2.1.0" "User Commands"
+
+.SH NAME
+Ray - assemble genomes in parallel using the message-passing interface
+.SH SYNOPSIS
+ mpiexec -n NUMBER_OF_RANKS Ray -k KMERLENGTH -p l1_1.fastq l1_2.fastq -p l2_1.fastq l2_2.fastq -o test
+
+ mpiexec -n NUMBER_OF_RANKS Ray Ray.conf # with commands in a file
+.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.
+
+ Ray targets several applications:
+
+ - de novo genome assembly (with Ray vanilla)
+ - 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)
+
+.SH OPTIONS
+
+ -help
+ Displays this help page.
+
+ -version
+ Displays Ray version and compilation options.
+
+ Using a configuration file
+
+ Ray can be launched with
+ mpiexec -n 16 Ray Ray.conf
+ The configuration file can include comments (starting with #).
+
+ K-mer length
+
+ -k kmerLength
+ 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.
+
+ Inputs
+
+ -p leftSequenceFile rightSequenceFile [averageOuterDistance standardDeviation]
+ Provides two files containing paired-end reads.
+ averageOuterDistance and standardDeviation are automatically computed if not provided.
+
+ -i interleavedSequenceFile [averageOuterDistance standardDeviation]
+ Provides one file containing interleaved paired-end reads.
+ averageOuterDistance and standardDeviation are automatically computed if not provided.
+
+ -s sequenceFile
+ Provides a file containing single-end reads.
+
+ Outputs
+
+ -o outputDirectory
+ Specifies the directory for outputted files. Default is RayOutput
+
+ Assembly options (defaults work well)
+
+ -disable-recycling
+ 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.
+ Sébastien Boisvert, Élénie Godzaridis, François Laviolette & Jacques Corbeil.
+ First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing, March 26-27 2011, Vancouver, BC, Canada.
+
+ -disable-scaffolder
+ Disables the scaffolder.
+
+ -minimum-contig-length minimumContigLength
+ Changes the minimum contig length, default is 100 nucleotides
+
+ -color-space
+ Runs in color-space
+ Needs csfasta files. Activated automatically if csfasta files are provided.
+
+ -use-maximum-seed-coverage maximumSeedCoverageDepth
+ Ignores any seed with a coverage depth above this threshold.
+ The default is 4294967295.
+
+ -use-minimum-seed-coverage minimumSeedCoverageDepth
+ Sets the minimum seed coverage depth.
+ Any path with a coverage depth lower than this will be discarded. The default is 0.
+
+ Distributed storage engine (all these values are for each MPI rank)
+
+ -bloom-filter-bits bits
+ Sets the number of bits for the Bloom filter
+ Default is 268435456 bits, 0 bits disables the Bloom filter.
+
+ -hash-table-buckets buckets
+ Sets the initial number of buckets. Must be a power of 2 !
+ Default value: 268435456
+
+ -hash-table-buckets-per-group buckets
+ Sets the number of buckets per group for sparse storage
+ Default value: 64, Must be between >=1 and <= 64
+
+ -hash-table-load-factor-threshold threshold
+ Sets the load factor threshold for real-time resizing
+ Default value: 0.75, must be >= 0.5 and < 1
+
+ -hash-table-verbosity
+ Activates verbosity for the distributed storage engine
+
+ Biological abundances
+
+ -search searchDirectory
+ 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
+
+ -one-color-per-file
+ 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.
+
+ Taxonomic profiling with colored de Bruijn graphs
+
+ -with-taxonomy Genome-to-Taxon.tsv TreeOfLife-Edges.tsv Taxon-Names.tsv
+ Provides a taxonomy.
+ Computes and writes detailed taxonomic profiles.
+ See Documentation/Taxonomy.txt for details.
+
+ -gene-ontology OntologyTerms.txt Annotations.txt
+ 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
+ Other outputs
+
+ -enable-neighbourhoods
+ Computes contig neighborhoods in the de Bruijn graph
+ Output file: RayOutput/NeighbourhoodRelations.txt
+
+ -amos
+ 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.
+
+ -write-kmers
+ Writes k-mer graph to RayOutput/kmers.txt
+ The resulting file is not utilised by Ray.
+ The resulting file is very large.
+
+ -write-read-markers
+ Writes read markers to disk.
+
+ -write-seeds
+ Writes seed DNA sequences to RayOutput/Rank<rank>.RaySeeds.fasta
+
+ -write-extensions
+ Writes extension DNA sequences to RayOutput/Rank<rank>.RayExtensions.fasta
+
+ -write-contig-paths
+ Writes contig paths with coverage values
+ to RayOutput/Rank<rank>.RayContigPaths.txt
+
+ -write-marker-summary
+ Writes marker statistics.
+
+ Memory usage
+
+ -show-memory-usage
+ Shows memory usage. Data is fetched from /proc on GNU/Linux
+ Needs __linux__
+
+ -show-memory-allocations
+ Shows memory allocation events
+
+ Algorithm verbosity
+
+ -show-extension-choice
+ Shows the choice made (with other choices) during the extension.
+
+ -show-ending-context
+ Shows the ending context of each extension.
+ Shows the children of the vertex where extension was too difficult.
+
+ -show-distance-summary
+ Shows summary of outer distances used for an extension path.
+
+ -show-consensus
+ Shows the consensus when a choice is done.
+
+ Checkpointing
+
+ -write-checkpoints checkpointDirectory
+ Write checkpoint files
+
+ -read-checkpoints checkpointDirectory
+ Read checkpoint files
+
+ -read-write-checkpoints checkpointDirectory
+ Read and write checkpoint files
+
+ Message routing for large number of cores
+
+ -route-messages
+ 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 -route-messages, 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
+
+ -connection-type type
+ Sets the connection type for routes.
+ Accepted values are debruijn, hypercube, polytope, group, random, kautz and complete. Default is debruijn.
+ 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: Erdős-Rényi 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
+ 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
+
+ -routing-graph-degree degree
+ Specifies the outgoing degree for the routing graph.
+ See Documentation/Routing.txt
+
+ Hardware testing
+
+ -test-network-only
+ Tests the network and returns.
+
+ -write-network-test-raw-data
+ Writes one additional file per rank detailing the network test.
+
+ -exchanges NumberOfExchanges
+ Sets the number of exchanges
+
+ -disable-network-test
+ Skips the network test.
+
+ Debugging
+
+ -verify-message-integrity
+ 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)
+
+ -run-profiler
+ Runs the profiler as the code runs. By default, only show granularity warnings.
+ Running the profiler increases running times.
+
+ -with-profiler-details
+ Shows number of messages sent and received in each methods during in each time slices (epochs). Needs -run-profiler.
+
+ -show-communication-events
+ Shows all messages sent and received.
+
+ -show-read-placement
+ Shows read placement in the graph during the extension.
+
+ -debug-bubbles
+ Debugs bubble code.
+ Bubbles can be due to heterozygous sites or sequencing errors or other (unknown) events
+
+ -debug-seeds
+ Debugs seed code.
+ Seeds are paths in the graph that are likely unique.
+
+ -debug-fusions
+ Debugs fusion code.
+
+ -debug-scaffolder
+ Debug the scaffolder.
+.SH FILES
+
+ Input files
+
+ Note: file format is determined with file extension.
+
+ .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)
+
+ Outputted files
+
+ Scaffolds
+
+ RayOutput/Scaffolds.fasta
+ The scaffold sequences in FASTA format
+ RayOutput/ScaffoldComponents.txt
+ The components of each scaffold
+ RayOutput/ScaffoldLengths.txt
+ The length of each scaffold
+ RayOutput/ScaffoldLinks.txt
+ Scaffold links
+
+ Contigs
+
+ RayOutput/Contigs.fasta
+ Contiguous sequences in FASTA format
+ RayOutput/ContigLengths.txt
+ The lengths of contiguous sequences
+
+ Summary
+
+ RayOutput/OutputNumbers.txt
+ Overall numbers for the assembly
+
+ de Bruijn graph
+
+ RayOutput/CoverageDistribution.txt
+ The distribution of coverage values
+ RayOutput/CoverageDistributionAnalysis.txt
+ Analysis of the coverage distribution
+ RayOutput/degreeDistribution.txt
+ Distribution of ingoing and outgoing degrees
+ RayOutput/kmers.txt
+ k-mer graph, required option: -write-kmers
+ The resulting file is not utilised by Ray.
+ The resulting file is very large.
+
+ Assembly steps
+
+ RayOutput/SeedLengthDistribution.txt
+ Distribution of seed length
+ RayOutput/Rank<rank>.OptimalReadMarkers.txt
+ Read markers.
+ RayOutput/Rank<rank>.RaySeeds.fasta
+ Seed DNA sequences, required option: -write-seeds
+ RayOutput/Rank<rank>.RayExtensions.fasta
+ Extension DNA sequences, required option: -write-extensions
+ RayOutput/Rank<rank>.RayContigPaths.txt
+ Contig paths with coverage values, required option: -write-contig-paths
+
+ Paired reads
+
+ RayOutput/LibraryStatistics.txt
+ Estimation of outer distances for paired reads
+ RayOutput/Library<LibraryNumber>.txt
+ Frequencies for observed outer distances (insert size + read lengths)
+
+ Partition
+
+ RayOutput/NumberOfSequences.txt
+ Number of reads in each file
+ RayOutput/SequencePartition.txt
+ Sequence partition
+
+ Ray software
+
+ RayOutput/RayVersion.txt
+ The version of Ray
+ RayOutput/RayCommand.txt
+ The exact same command provided
+
+ AMOS
+
+ RayOutput/AMOS.afg
+ Assembly representation in AMOS format, required option: -amos
+
+ Communication
+
+ RayOutput/MessagePassingInterface.txt
+ Number of messages sent
+ RayOutput/NetworkTest.txt
+ Latencies in microseconds
+ RayOutput/Rank<rank>NetworkTestData.txt
+ Network test raw data
+.SH DOCUMENTATION
+
+ - mpiexec -n 1 Ray -help|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
+.SH AUTHOR
+ Written by Sébastien Boisvert.
+.SH "REPORTING BUGS"
+ Report bugs to denovoassembler-users@lists.sourceforge.net
+ Home page: <http://denovoassembler.sourceforge.net/>
+.SH COPYRIGHT
+ 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.
+
+ 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.
+
+ You have received a copy of the GNU General Public License
+ along with this program (see LICENSE).
+
