Desired coverage, as a number of bases, can be set using the new configuration parameter - Reads.desiredCoverage. This value will be auto-generated by the GenerateConfig.py script (different PR).
If there isn't enough coverage available with reads longer than Reads.minReadLength, the program will abort.
If more than desired coverage is available with reads longer than Reads.minReadLength, then Shasta will increase the value of minReadLength to arrive close to the desired coverage
Reads.desiredCoverage can take values specified as
raw number of bases. E.g --Reads.desiredCoverage 2000000000
kilo bases (K, Kb, Kbp). E.g. --Reads.desiredCoverage 2000000Kb
mega bases (M, Mb, Mbp). E.g. --Reads.desiredCoverage 2000Mb
giga bases (G, Gb, Gbp). E.g. --Reads.desiredCoverage 2Gb
Performance hit: For HG002-Guppy-3.6.0.fasta dropping coverage to 120G adds a little over 2 minutes to the assembly time.
Desired coverage, as a number of bases, can be set using the new configuration parameter - Reads.desiredCoverage. This value will be auto-generated by the GenerateConfig.py script (different PR).
Reads.desiredCoveragecan take values specified as--Reads.desiredCoverage 2000000000--Reads.desiredCoverage 2000000Kb--Reads.desiredCoverage 2000Mb--Reads.desiredCoverage 2GbPerformance hit: For
HG002-Guppy-3.6.0.fastadropping coverage to120Gadds a little over 2 minutes to the assembly time.