Canu-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.2

Author / Distributor

Canu

Description

"Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). " More details are at Canu's documentation.

Running Program

Version 2.2

To use this version, please load the module with

ml canu/2.2-GCCcore-11.2.0.lua

When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 . The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.

Here is an example of a shell script, sub.sh, to run Canu on the batch queue:

#!/bin/bash
#SBATCH --partition=batch
#SBATCH --job-name=canujobname
#SBATCH --ntasks=1
#SBATCH --time=1:00:00
#SBATCH --mem=10G

cd $SLURM_SUBMIT_DIR

ml canu/2.2-GCCcore-11.2.0.lua

canu gridOptions=" --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 " [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. Please note that the Slurm headers (#SBATCH lines) are only for Canu's initial job. The resource limits of all of the jobs that Canu spawns will be determined by what is defined in the gridOptions.

To submit the job submission use the command:

sbatch ./sub.sh 

Documentation

[cft07037@d2-13 canu]$ ml canu/2.2-GCCcore-11.2.0 
[cft07037@d2-13 canu]$ canu --help

usage:   canu [-version] [-citation] \
              [-haplotype | -correct | -trim | -assemble | -trim-assemble] \
              [-s <assembly-specifications-file>] \
               -p <assembly-prefix> \
               -d <assembly-directory> \
               genomeSize=<number>[g|m|k] \
              [other-options] \
              [-haplotype{NAME} illumina.fastq.gz] \
              [-corrected] \
              [-trimmed] \
              [-pacbio |
               -nanopore |
               -pacbio-hifi] file1 file2 ...

example: canu -d run1 -p godzilla genomeSize=1g -nanopore-raw reads/*.fasta.gz 


  To restrict canu to only a specific stage, use:
    -haplotype     - generate haplotype-specific reads
    -correct       - generate corrected reads
    -trim          - generate trimmed reads
    -assemble      - generate an assembly
    -trim-assemble - generate trimmed reads and then assemble them

  The assembly is computed in the -d <assembly-directory>, with output files named
  using the -p <assembly-prefix>.  This directory is created if needed.  It is not
  possible to run multiple assemblies in the same directory.

  The genome size should be your best guess of the haploid genome size of what is being
  assembled.  It is used primarily to estimate coverage in reads, NOT as the desired
  assembly size.  Fractional values are allowed: '4.7m' equals '4700k' equals '4700000'

  Some common options:
    useGrid=string
      - Run under grid control (true), locally (false), or set up for grid control
        but don't submit any jobs (remote)
    rawErrorRate=fraction-error
      - The allowed difference in an overlap between two raw uncorrected reads.  For lower
        quality reads, use a higher number.  The defaults are 0.300 for PacBio reads and
        0.500 for Nanopore reads.
    correctedErrorRate=fraction-error
      - The allowed difference in an overlap between two corrected reads.  Assemblies of
        low coverage or data with biological differences will benefit from a slight increase
        in this.  Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads.
    gridOptions=string
      - Pass string to the command used to submit jobs to the grid.  Can be used to set
        maximum run time limits.  Should NOT be used to set memory limits; Canu will do
        that for you.
    minReadLength=number
      - Ignore reads shorter than 'number' bases long.  Default: 1000.
    minOverlapLength=number
      - Ignore read-to-read overlaps shorter than 'number' bases long.  Default: 500.
  A full list of options can be printed with '-options'.  All options can be supplied in
  an optional sepc file with the -s option.

  For TrioCanu, haplotypes are specified with the -haplotype{NAME} option, with any
  number of haplotype-specific Illumina read files after.  The {NAME} of each haplotype
  is free text (but only letters and numbers, please).  For example:
    -haplotypeNANNY nanny/*gz
    -haplotypeBILLY billy1.fasta.gz billy2.fasta.gz

  Reads can be either FASTA or FASTQ format, uncompressed, or compressed with gz, bz2 or xz.

  Reads are specified by the technology they were generated with, and any processing performed.

  [processing]
    -corrected
    -trimmed

  [technology]
    -pacbio      <files>
    -nanopore    <files>
    -pacbio-hifi <files>

Complete documentation at http://canu.readthedocs.org/en/latest/

[cft07037@d2-13 canu]$ ml canu/2.2-GCCcore-11.2.0 
[cft07037@d2-13 canu]$ canu -options
batConcurrency                     Unused, only one process supported
batMemory                          Approximate maximum memory usage, in gigabytes, default is the maxMemory limit
batOptions                         Advanced options to bogart
batStageSpace                      Amount of local disk space needed to stage data for unitig construction jobs
batThreads                         Number of threads to use; default is the maxThreads limit
cnsConcurrency                     If grid not enabled, number of unitig consensus jobs to run at the same time; default is n_proc / n_threads
cnsConsensus                       Which consensus algorithm to use; 'pbdagcon' (fast, reliable); 'utgcns' (multialignment output); 'quick' (single read mosaic); default 'pbdagcon'
cnsErrorRate                       Consensus expects alignments at about this error rate
cnsMaxCoverage                     Limit unitig consensus to at most this coverage; default '40' = unlimited
cnsMemory                          Amount of memory, in gigabytes, to use for unitig consensus jobs
cnsPartitions                      Attempt to create this many consensus jobs; default '0' = based on the largest tig
cnsStageSpace                      Amount of local disk space needed to stage data for unitig consensus jobs
cnsThreads                         Number of threads to use for unitig consensus jobs
contigFilter                       Parameters to filter out 'unassembled' unitigs.  Five values: minReads minLength singleReadSpan lowCovFraction lowCovDepth
corConcurrency                     If grid not enabled, number of read correction jobs to run at the same time; default is n_proc / n_threads
corConsensus                       Which consensus algorithm to use; only 'falcon' is supported; default 'falcon'
corErrorRate                       Only use raw alignments below this error rate to construct corrected reads
corFilter                          Method to filter short reads from correction; 'quick' or 'expensive'; default 'expensive'
corMaxEvidenceCoverageGlobal       Limit reads used for correction to supporting at most this coverage; default: '1.0x' = 1.0 * estimated coverage
corMaxEvidenceCoverageLocal        Limit reads being corrected to at most this much evidence coverage; default: '2.0x' = 2.0 * estimated coverage
corMaxEvidenceErate                Limit read correction to only overlaps at or below this fraction error; default: unlimited
corMemory                          Amount of memory, in gigabytes, to use for read correction jobs
corMhapBlockSize                   Number of reads per GB of memory allowed (mhapMemory)
cormhapConcurrency                 If grid not enabled, number of mhap overlaps for correction jobs to run at the same time; default is n_proc / n_threads
corMhapFilterThreshold             Value between 0 and 1. kmers which comprise more than this percentage of the input are downweighted
corMhapFilterUnique                Expert option: True or false, supress the low-frequency k-mer distribution based on them being likely noise and not true overlaps. Threshold auto-computed based on error rate and coverage.
cormhapMemory                      Amount of memory, in gigabytes, to use for mhap overlaps for correction jobs
corMhapMerSize                     K-mer size for seeds in mhap
corMhapNoTf                        Expert option: True or false, do not use tf weighting, only idf of tf-idf.
corMhapOptions                     Expert option: free-form parameters to pass to MHAP.
corMhapOrderedMerSize              K-mer size for second-stage filter in mhap
corMhapPipe                        Report results to a pipe instead of *large* files.
corMhapSensitivity                 Coarse sensitivity level: 'low', 'normal' or 'high'.  Set automatically based on coverage; 'high' <= 30x < 'normal' < 60x <= 'low'
cormhapStageSpace                  Amount of local disk space needed to stage data for mhap overlaps for correction jobs
cormhapThreads                     Number of threads to use for mhap overlaps for correction jobs
corMhapVersion                     Version of the MHAP jar file to use
corMinCoverage                     Minimum number of bases supporting each corrected base, if less than this sequences are split; default based on input read coverage: 0 <= 30x < 4 < 60x <= 4
corMinEvidenceLength               Limit read correction to only overlaps longer than this; default: unlimited
corMMapBlockSize                   Number of reads per 1GB; memory * blockSize = the size of  block loaded into memory per job
cormmapConcurrency                 If grid not enabled, number of mmap overlaps for correction jobs to run at the same time; default is n_proc / n_threads
cormmapMemory                      Amount of memory, in gigabytes, to use for mmap overlaps for correction jobs
corMMapMerSize                     K-mer size for seeds in minmap
cormmapStageSpace                  Amount of local disk space needed to stage data for mmap overlaps for correction jobs
cormmapThreads                     Number of threads to use for mmap overlaps for correction jobs
corOutCoverage                     Only correct the longest reads up to this coverage; default 40
corOverlapper                      Which overlap algorithm to use for correction
corovlConcurrency                  If grid not enabled, number of overlaps for correction jobs to run at the same time; default is n_proc / n_threads
corOvlErrorRate                    Overlaps above this error rate are not computed
corOvlFilter                       Filter overlaps based on expected kmers vs observed kmers
corOvlFrequentMers                 Do not seed overlaps with these kmers
corOvlHashBits                     Width of the kmer hash.  Width 22=1gb, 23=2gb, 24=4gb, 25=8gb.  Plus 10b per corOvlHashBlockLength
corOvlHashBlockLength              Amount of sequence (bp) to load into the overlap hash table
corOvlHashLoad                     Maximum hash table load.  If set too high, table lookups are inefficent; if too low, search overhead dominates run time; default 0.75
corovlMemory                       Amount of memory, in gigabytes, to use for overlaps for correction jobs
corOvlMerDistinct                  K-mer frequency threshold; the least frequent fraction of distinct mers can seed overlaps
corOvlMerSize                      K-mer size for seeds in overlaps
corOvlMerThreshold                 K-mer frequency threshold; mers more frequent than this count are ignored
corOvlRefBlockLength               Amount of sequence (bp) to search against the hash table per batch
corovlStageSpace                   Amount of local disk space needed to stage data for overlaps for correction jobs
corovlThreads                      Number of threads to use for overlaps for correction jobs
corPartitionMin                    Don't make a read correction partition with fewer than N reads
corPartitions                      Partition read correction into N jobs
corReAlign                         Refine overlaps by computing the actual alignment: 'true' or 'false'.  Not useful for overlapper=ovl.  Uses corOvlErrorRate
correctedErrorRate                 Expected fraction error in an alignment of two corrected reads
corStageSpace                      Amount of local disk space needed to stage data for read correction jobs
corThreads                         Number of threads to use for read correction jobs
enableOEA                          Do overlap error adjustment - comprises two steps: read error detection (RED) and overlap error adjustment (OEA); default 'true'
executiveMemory                    Amount of memory, in GB, to reserve for the Canu exective process
executiveThreads                   Number of threads to reserve for the Canu exective process
genomeSize                         An estimate of the size of the genome
gnuplot                            Path to the gnuplot executable
gnuplotImageFormat                 Image format that gnuplot will generate.  Default: based on gnuplot, 'png', 'svg' or 'gif'
gridEngine                         Grid engine configuration, not documented
gridEngineArrayMaxJobs             Grid engine configuration, not documented
gridEngineArrayName                Grid engine configuration, not documented
gridEngineArrayOption              Grid engine configuration, not documented
gridEngineArraySubmitID            Grid engine configuration, not documented
gridEngineJobID                    Grid engine configuration, not documented
gridEngineMemoryOption             Grid engine configuration, not documented
gridEngineMemoryPerJob             Grid engine configuration, not documented
gridEngineMemoryUnits              Grid engine configuration, not documented
gridEngineNameOption               Grid engine configuration, not documented
gridEngineNameToJobIDCommand       Grid engine configuration, not documented
gridEngineNameToJobIDCommandNoArrayGrid engine configuration, not documented
gridEngineOutputOption             Grid engine configuration, not documented
gridEngineResourceOption           Grid engine configuration, not documented
gridEngineStageOption              Grid engine configuration, not documented
gridEngineSubmitCommand            Grid engine configuration, not documented
gridEngineTaskID                   Grid engine configuration, not documented
gridEngineThreadsOption            Grid engine configuration, not documented
gridOptions                        Grid engine options applied to all jobs
gridOptionsbat                     Grid engine options applied to unitig construction jobs
gridOptionscns                     Grid engine options applied to unitig consensus jobs
gridOptionscor                     Grid engine options applied to read correction jobs
gridOptionscormhap                 Grid engine options applied to mhap overlaps for correction jobs
gridOptionscormmap                 Grid engine options applied to mmap overlaps for correction jobs
gridOptionscorovl                  Grid engine options applied to overlaps for correction jobs
gridOptionsExecutive               Grid engine options applied to the canu executive script
gridOptionshap                     Grid engine options applied to haplotype assignment jobs
gridOptionsJobName                 Grid jobs job-name suffix
gridOptionsmeryl                   Grid engine options applied to mer counting jobs
gridOptionsobtmhap                 Grid engine options applied to mhap overlaps for trimming jobs
gridOptionsobtmmap                 Grid engine options applied to mmap overlaps for trimming jobs
gridOptionsobtovl                  Grid engine options applied to overlaps for trimming jobs
gridOptionsoea                     Grid engine options applied to overlap error adjustment jobs
gridOptionsovb                     Grid engine options applied to overlap store bucketizing jobs
gridOptionsovs                     Grid engine options applied to overlap store sorting jobs
gridOptionsred                     Grid engine options applied to read error detection jobs
gridOptionsutgmhap                 Grid engine options applied to mhap overlaps for unitig construction jobs
gridOptionsutgmmap                 Grid engine options applied to mmap overlaps for unitig construction jobs
gridOptionsutgovl                  Grid engine options applied to overlaps for unitig construction jobs
hapConcurrency                     Unused, there is only one process
hapMemory                          Amount of memory, in gigabytes, to use for haplotype assignment
hapStageSpace                      Amount of local disk space needed to stage data for haplotype assignment jobs
hapThreads                         Number of threads to use for haplotype assignment
hapUnknownFraction                 Fraction of allowed unknown bases before they are included in the assembly, between 0-1; default 0.05
homoPolyCompress                   Compute everything but consensus sequences using homopolymer compressed reads
java                               Java interpreter to use; at least version 1.8; default 'java'
javaUse64Bit                       Java interpreter supports the -d64 or -d32 flags; default auto
maxInputCoverage                   If input coverage is high, downsample to something reasonable; default 200
maxMemory                          Maximum memory to use by any component of the assembler
maxThreads                         Maximum number of compute threads to use by any component of the assembler
merylConcurrency                   Unused, there is only one process
merylMemory                        Amount of memory, in gigabytes, to use for mer counting
merylStageSpace                    Amount of local disk space needed to stage data for mer counting jobs
merylThreads                       Number of threads to use for mer counting
minimap                            Path to minimap2; default 'minimap2'
minInputCoverage                   Stop if input coverage is too low; default 10
minMemory                          Minimum amount of memory needed to compute the assembly (do not set unless prompted!)
minOverlapLength                   Overlaps shorter than this length are not computed; default 500
minReadLength                      Reads shorter than this length are not loaded into the assembler; default 1000
minThreads                         Minimum number of compute threads suggested to compute the assembly
objectStore                        Type of object storage used; not ready for production yet
objectStoreClient                  Path to the command line client used to access the object storage
objectStoreClientDA                Path to the command line client used to download files from object storage
objectStoreClientUA                Path to the command line client used to upload files to object storage
objectStoreNameSpace               Object store parameters; specific to the type of objectStore used
objectStoreProject                 Object store project; specific to the type of objectStore used
obtErrorRate                       Stringency of overlaps to use for trimming
obtMhapBlockSize                   Number of reads per GB of memory allowed (mhapMemory)
obtmhapConcurrency                 If grid not enabled, number of mhap overlaps for trimming jobs to run at the same time; default is n_proc / n_threads
obtMhapFilterThreshold             Value between 0 and 1. kmers which comprise more than this percentage of the input are downweighted
obtMhapFilterUnique                Expert option: True or false, supress the low-frequency k-mer distribution based on them being likely noise and not true overlaps. Threshold auto-computed based on error rate and coverage.
obtmhapMemory                      Amount of memory, in gigabytes, to use for mhap overlaps for trimming jobs
obtMhapMerSize                     K-mer size for seeds in mhap
obtMhapNoTf                        Expert option: True or false, do not use tf weighting, only idf of tf-idf.
obtMhapOptions                     Expert option: free-form parameters to pass to MHAP.
obtMhapOrderedMerSize              K-mer size for second-stage filter in mhap
obtMhapPipe                        Report results to a pipe instead of *large* files.
obtMhapSensitivity                 Coarse sensitivity level: 'low', 'normal' or 'high'.  Set automatically based on coverage; 'high' <= 30x < 'normal' < 60x <= 'low'
obtmhapStageSpace                  Amount of local disk space needed to stage data for mhap overlaps for trimming jobs
obtmhapThreads                     Number of threads to use for mhap overlaps for trimming jobs
obtMhapVersion                     Version of the MHAP jar file to use
obtMMapBlockSize                   Number of reads per 1GB; memory * blockSize = the size of  block loaded into memory per job
obtmmapConcurrency                 If grid not enabled, number of mmap overlaps for trimming jobs to run at the same time; default is n_proc / n_threads
obtmmapMemory                      Amount of memory, in gigabytes, to use for mmap overlaps for trimming jobs
obtMMapMerSize                     K-mer size for seeds in minmap
obtmmapStageSpace                  Amount of local disk space needed to stage data for mmap overlaps for trimming jobs
obtmmapThreads                     Number of threads to use for mmap overlaps for trimming jobs
obtOverlapper                      Which overlap algorithm to use for overlap based trimming
obtovlConcurrency                  If grid not enabled, number of overlaps for trimming jobs to run at the same time; default is n_proc / n_threads
obtOvlErrorRate                    Overlaps at or below this error rate are used to trim reads
obtOvlFilter                       Filter overlaps based on expected kmers vs observed kmers
obtOvlFrequentMers                 Do not seed overlaps with these kmers
obtOvlHashBits                     Width of the kmer hash.  Width 22=1gb, 23=2gb, 24=4gb, 25=8gb.  Plus 10b per obtOvlHashBlockLength
obtOvlHashBlockLength              Amount of sequence (bp) to load into the overlap hash table
obtOvlHashLoad                     Maximum hash table load.  If set too high, table lookups are inefficent; if too low, search overhead dominates run time; default 0.75
obtovlMemory                       Amount of memory, in gigabytes, to use for overlaps for trimming jobs
obtOvlMerDistinct                  K-mer frequency threshold; the least frequent fraction of distinct mers can seed overlaps
obtOvlMerSize                      K-mer size for seeds in overlaps
obtOvlMerThreshold                 K-mer frequency threshold; mers more frequent than this count are ignored
obtOvlRefBlockLength               Amount of sequence (bp) to search against the hash table per batch
obtovlStageSpace                   Amount of local disk space needed to stage data for overlaps for trimming jobs
obtovlThreads                      Number of threads to use for overlaps for trimming jobs
obtReAlign                         Refine overlaps by computing the actual alignment: 'true' or 'false'.  Not useful for overlapper=ovl.  Uses obtOvlErrorRate
oeaBatchLength                     Number of bases per overlap error correction batch
oeaBatchSize                       Number of reads per overlap error correction batch
oeaConcurrency                     If grid not enabled, number of overlap error adjustment jobs to run at the same time; default is n_proc / n_threads
oeaErrorRate                       Only use overlaps with at most this much fraction error to find errors in reads; default utgOvlErrorRate, 0.003 for HiFi reads
oeaHaploConfirm                    This many or more reads will confirm a true haplotype difference; default 5
oeaMaskTrivial                     Mask trivial DNA in Overlap Error Adjustment; default off; on for HiFi reads
oeaMemory                          Amount of memory, in gigabytes, to use for overlap error adjustment jobs
oeaStageSpace                      Amount of local disk space needed to stage data for overlap error adjustment jobs
oeaThreads                         Number of threads to use for overlap error adjustment jobs
onFailure                          Full path to command to run on failure
onSuccess                          Full path to command to run on successful completion
ovbConcurrency                     If grid not enabled, number of overlap store bucketizing jobs to run at the same time; default is n_proc / n_threads
ovbMemory                          Amount of memory, in gigabytes, to use for overlap store bucketizing jobs
ovbStageSpace                      Amount of local disk space needed to stage data for overlap store bucketizing jobs
ovbThreads                         Number of threads to use for overlap store bucketizing jobs
ovsConcurrency                     If grid not enabled, number of overlap store sorting jobs to run at the same time; default is n_proc / n_threads
ovsMemory                          Amount of memory, in gigabytes, to use for overlap store sorting jobs
ovsStageSpace                      Amount of local disk space needed to stage data for overlap store sorting jobs
ovsThreads                         Number of threads to use for overlap store sorting jobs
preExec                            A command line to run at the start of Canu execution scripts
purgeOverlaps                      When to delete intermediate overlap files: never, normal (default), aggressive, dangerous
rawErrorRate                       Expected fraction error in an alignment of two uncorrected reads
readSamplingBias                   Score reads as 'random * length^bias', keep the highest scoring reads
redBatchLength                     Number of bases per fragment error detection batch
redBatchSize                       Number of reads per fragment error detection batch
redConcurrency                     If grid not enabled, number of read error detection jobs to run at the same time; default is n_proc / n_threads
redMemory                          Amount of memory, in gigabytes, to use for read error detection jobs
redStageSpace                      Amount of local disk space needed to stage data for read error detection jobs
redThreads                         Number of threads to use for read error detection jobs
saveMerCounts                      Save full mer counting results, sometimes useful
saveOverlaps                       Do not remove the overlap stores.  Default: false = remove overlap stores when they're no longer needed
saveReadCorrections                Save intermediate read correction files, almost never a good idea
saveReadHaplotypes                 Save intermediate read haplotype files, almost never a good idea
saveReads                          Save intermediate corrected and trimmed reads to asm.correctedReads.fasta.gz and asm.trimmedReads.fasta.gz
shell                              Command interpreter to use; sh-compatible (e.g., bash), NOT C-shell (csh or tcsh); default '/bin/sh'
showNext                           Don't run any commands, just report what would run
stageDirectory                     If set, copy heavily used data to this node-local location
stopAfter                          Stop after a specific algorithm step is completed
stopOnLowCoverage                  Stop if raw, corrected or trimmed read coverage is low
trimReadsCoverage                  Minimum depth of evidence to retain bases; default '2
trimReadsOverlap                   Minimum overlap between evidence to make contiguous trim; default '500'
unitigger                          Which unitig algorithm to use; only 'bogart' supported; default 'bogart'
useGrid                            If 'true', enable grid-based execution; if 'false', run all jobs on the local machine; if 'remote', create jobs for grid execution but do not submit; default 'true'
useGridbat                         If 'true', run module unitig construction under grid control; if 'false' run locally.
useGridcns                         If 'true', run module unitig consensus under grid control; if 'false' run locally.
useGridcor                         If 'true', run module read correction under grid control; if 'false' run locally.
useGridcormhap                     If 'true', run module mhap overlaps for correction under grid control; if 'false' run locally.
useGridcormmap                     If 'true', run module mmap overlaps for correction under grid control; if 'false' run locally.
useGridcorovl                      If 'true', run module overlaps for correction under grid control; if 'false' run locally.
useGridhap                         If 'true', run module haplotype assignment under grid control; if 'false' run locally.
useGridmeryl                       If 'true', run module mer counting under grid control; if 'false' run locally.
useGridobtmhap                     If 'true', run module mhap overlaps for trimming under grid control; if 'false' run locally.
useGridobtmmap                     If 'true', run module mmap overlaps for trimming under grid control; if 'false' run locally.
useGridobtovl                      If 'true', run module overlaps for trimming under grid control; if 'false' run locally.
useGridoea                         If 'true', run module overlap error adjustment under grid control; if 'false' run locally.
useGridovb                         If 'true', run module overlap store bucketizing under grid control; if 'false' run locally.
useGridovs                         If 'true', run module overlap store sorting under grid control; if 'false' run locally.
useGridred                         If 'true', run module read error detection under grid control; if 'false' run locally.
useGridutgmhap                     If 'true', run module mhap overlaps for unitig construction under grid control; if 'false' run locally.
useGridutgmmap                     If 'true', run module mmap overlaps for unitig construction under grid control; if 'false' run locally.
useGridutgovl                      If 'true', run module overlaps for unitig construction under grid control; if 'false' run locally.
utgBubbleDeviation                 Overlaps this much above mean of contig will be used to identify bubbles
utgChimeraType                     When to filter reads for contig construction: none, chimera (missing middle), uncovered (missing middle or ends), deadend (missing middle or end or no neighbor) (default)
utgErrorRate                       Overlaps at or below this error rate are used to construct contigs
utgGraphDeviation                  Overlaps this much above median will not be used for initial graph construction
utgMhapBlockSize                   Number of reads per GB of memory allowed (mhapMemory)
utgmhapConcurrency                 If grid not enabled, number of mhap overlaps for unitig construction jobs to run at the same time; default is n_proc / n_threads
utgMhapFilterThreshold             Value between 0 and 1. kmers which comprise more than this percentage of the input are downweighted
utgMhapFilterUnique                Expert option: True or false, supress the low-frequency k-mer distribution based on them being likely noise and not true overlaps. Threshold auto-computed based on error rate and coverage.
utgmhapMemory                      Amount of memory, in gigabytes, to use for mhap overlaps for unitig construction jobs
utgMhapMerSize                     K-mer size for seeds in mhap
utgMhapNoTf                        Expert option: True or false, do not use tf weighting, only idf of tf-idf.
utgMhapOptions                     Expert option: free-form parameters to pass to MHAP.
utgMhapOrderedMerSize              K-mer size for second-stage filter in mhap
utgMhapPipe                        Report results to a pipe instead of *large* files.
utgMhapSensitivity                 Coarse sensitivity level: 'low', 'normal' or 'high'.  Set automatically based on coverage; 'high' <= 30x < 'normal' < 60x <= 'low'
utgmhapStageSpace                  Amount of local disk space needed to stage data for mhap overlaps for unitig construction jobs
utgmhapThreads                     Number of threads to use for mhap overlaps for unitig construction jobs
utgMhapVersion                     Version of the MHAP jar file to use
utgMMapBlockSize                   Number of reads per 1GB; memory * blockSize = the size of  block loaded into memory per job
utgmmapConcurrency                 If grid not enabled, number of mmap overlaps for unitig construction jobs to run at the same time; default is n_proc / n_threads
utgmmapMemory                      Amount of memory, in gigabytes, to use for mmap overlaps for unitig construction jobs
utgMMapMerSize                     K-mer size for seeds in minmap
utgmmapStageSpace                  Amount of local disk space needed to stage data for mmap overlaps for unitig construction jobs
utgmmapThreads                     Number of threads to use for mmap overlaps for unitig construction jobs
utgOverlapper                      Which overlap algorithm to use for unitig construction
utgovlConcurrency                  If grid not enabled, number of overlaps for unitig construction jobs to run at the same time; default is n_proc / n_threads
utgOvlErrorRate                    Overlaps at or below this error rate are used to trim reads
utgOvlFilter                       Filter overlaps based on expected kmers vs observed kmers
utgOvlFrequentMers                 Do not seed overlaps with these kmers
utgOvlHashBits                     Width of the kmer hash.  Width 22=1gb, 23=2gb, 24=4gb, 25=8gb.  Plus 10b per utgOvlHashBlockLength
utgOvlHashBlockLength              Amount of sequence (bp) to load into the overlap hash table
utgOvlHashLoad                     Maximum hash table load.  If set too high, table lookups are inefficent; if too low, search overhead dominates run time; default 0.75
utgovlMemory                       Amount of memory, in gigabytes, to use for overlaps for unitig construction jobs
utgOvlMerDistinct                  K-mer frequency threshold; the least frequent fraction of distinct mers can seed overlaps
utgOvlMerSize                      K-mer size for seeds in overlaps
utgOvlMerThreshold                 K-mer frequency threshold; mers more frequent than this count are ignored
utgOvlRefBlockLength               Amount of sequence (bp) to search against the hash table per batch
utgovlStageSpace                   Amount of local disk space needed to stage data for overlaps for unitig construction jobs
utgovlThreads                      Number of threads to use for overlaps for unitig construction jobs
utgReAlign                         Refine overlaps by computing the actual alignment: 'true' or 'false'.  Not useful for overlapper=ovl.  Uses utgOvlErrorRate
utgRepeatConfusedBP                Repeats where the next best edge is at least this many bp shorter will not be split
utgRepeatConfusedPC                Repeats where the next best edge is at least this many percent shorter will not be split
utgRepeatDeviation                 Overlaps this much above mean unitig error rate will not be used for repeat splitting

Back to Top

Installation

Source code obtained from https://github.com/marbl/canu/releases/download/v2.2

System

64-bit Linux