Hello!
Could you comment on when one might want to toy with the coverage options
to Ray, and what sort of expected effects these would have
Assembly options (defaults work well)
-minimumCoverage minimumCoverage
Sets manually the minimum coverage.
If not provided, it is computed by Ray automatically.
-peakCoverage peakCoverage
Sets manually the peak coverage.
If not provided, it is computed by Ray automatically.
-repeatCoverage repeatCoverage
Sets manually the repeat coverage.
If not provided, it is computed by Ray automatically.
For a single genome dataset, the CoverageDistribution file:
k-mer length: 21
Lowest coverage observed: 2
MinimumCoverage: 14
PeakCoverage: 58
RepeatCoverage: 102
Number of k-mers with at least MinimumCoverage: 17633562 k-mers
Percentage of vertices with coverage 2: 29.714 %
For a large metagenomic dataset, the CoverageDistribution file:
k-mer length: 21
Lowest coverage observed: 2
MinimumCoverage: 240
PeakCoverage: 241
RepeatCoverage: 242
Number of k-mers with at least MinimumCoverage: 11446138 k-mers
Percentage of vertices with coverage 2: 17.4967 %
Looking at these, I'm now confused by the MinimumCoverage value -- in my
metagenomic example it is quite high. Is this setting the minimum coverage
to be included in a contig?
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