This adds a simple method for evaluating the alignment drift, skip, trim, alignedFraction, and markerCount during run time, and choosing cutoffs based on a percentile. Testing on 3 basecallers and 1 ultralong dataset confirms that performance in terms of continuity and total assembled length is equal to or better than manually selected parameters.
For future development, more CSV output files are created when running with ReadGraph.creationMethod 2. This includes the distribution of all (5) parameters that are currently automated, as well as a list of alignments and their individual stats regarding these parameters.
maxTrim is currently still being evaluated, so perhaps it is best to wait on merging until those results are in.
2 new config files are added, which enable automation:
Nanopore-Jun2020-Automation.conf
Nanopore-UL-Jun2020-Automation.conf
The major changes to these config files are:
Substitute maxSkip, maxDrift, maxTrim, minAlignedMarkerCount, and minAlignedFraction for very permissive values
Enable ReadGraph.CreationMethod 2
Enable MarkerGraph.maxCoverage 0, which automates marker vertex coverage thresholding using PeakFinder
Remove ReadGraph.maxAlignmentCount 12 from the UL config (as a result of testing)
This adds a simple method for evaluating the alignment drift, skip, trim, alignedFraction, and markerCount during run time, and choosing cutoffs based on a percentile. Testing on 3 basecallers and 1 ultralong dataset confirms that performance in terms of continuity and total assembled length is equal to or better than manually selected parameters.
For future development, more CSV output files are created when running with
ReadGraph.creationMethod 2. This includes the distribution of all (5) parameters that are currently automated, as well as a list of alignments and their individual stats regarding these parameters.maxTrim is currently still being evaluated, so perhaps it is best to wait on merging until those results are in.
2 new config files are added, which enable automation:
The major changes to these config files are:
maxSkip,maxDrift,maxTrim,minAlignedMarkerCount, andminAlignedFractionfor very permissive valuesReadGraph.CreationMethod 2MarkerGraph.maxCoverage 0, which automates marker vertex coverage thresholding using PeakFinderReadGraph.maxAlignmentCount 12from the UL config (as a result of testing)