CONSENT 2.2.2
Contents
Conda
See the ‘activating the conda environment’ section below to access this
software.
CONSENT-2.2.2
CONSENT (Scalable long read self-correction and assembly polishing with multiple sequence alignment) is a self-correction method for long reads. It works by, first, computing overlaps between the long reads, in order to define an alignment pile (i.e. a set of overlapping reads used for correction) for each read. Each read’s alignment pile is then further divided into smaller windows, that are corrected idependently. First, a multiple alignment strategy is used in order to compute consensus. Then, this consensus is further polished with a local de Bruijn graph, in order to get rid of the remaining errors. Additionally to error correction, CONSENT can also perform assembly polishing.
Running CONSENT
Self-correction
To run CONSENT for long reads self-correction, run the following command:
./CONSENT-correct --in longReads.fast[a|q] --out result.fasta --type readsTechnology
- longReads.fast[a|q]: fasta or fastq file of long reads to .
- result.fasta: fasta file where to output the corrected long reads.
- readsTechnology: Indicate whether the long reads are from PacBio (–type PB) or Oxford Nanopore (–type ONT)
Polishing
To run CONSENT for assembly polishing, run the followning command:
./CONSENT-polish --contigs contigs.fast[a|q] --reads longReads.fast[a|q] --out result.fasta
- contigs.fast[a|q]: fasta or fastq file of contigs to polish.
- longReads.fast[a|q]: fasta or fastq file of long reads to use for polishing.
- result.fasta: fasta file where to output the polished contigs.
Options
--windowSize INT, -l INT: Size of the windows to process. (default: 500)
--minSupport INT, -s INT: Minimum support to consider a window for correction. (default: 4)
--maxSupport INT, -S INT: Maximum number of overlaps to include in a pile. (default: 150)
--maxMSA INT, -M: Maximum number of sequences to include into the MSA. (default: 150)
--merSize INT, -k INT: k-mer size for chaining and polishing. (default: 9)
--solid INT, -f INT: Minimum number of occurrences to consider a k-mer as solid during polishing. (default: 4)
--anchorSupport INT, -c INT: Minimum number of sequences supporting (Ai) - (Ai+1) to keep the two anchors in the chaining. (default: 8)
--minAnchors INT, -a INT: Minimum number of anchors in a window to allow consensus computation. (default: 2)
--windowOverlap INT, -o INT: Overlap size between consecutive windows. (default: 50)
--nproc INT, -j INT: Number of processes to run in parallel (default: number of cores).
--minimapIndex INT, -m INT: Split minimap2 index every INT input bases (default: 500M).
--tmpdir STRING, -t STRING: Path where to store the temporary overlaps file (default: working directory, as Alignments_dateTimeStamp.paf).
--help, -h: Print this help message.
Activating the conda environment
Check out a node with qrsh and run
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To run over SGE, include the source line above in your shell script prior to
the CONSENT commands.
Location and version
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help message
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software ref: https://github.com/morispi/CONSENT
research ref: https://doi.org/10.1038/s41598-020-80757-5