Setting of parameters "corMhapSensitivity", "corMaxEvidenceCoverageLocal", "corMaxEvidenceCoverageGlobal", "oeaMemory", "redMemory", "batMemory"

[B-1991-ing]

Dear Canu team,

I recently want to use CANU for my metagenome assembly in three separate steps like below, but I don't know which step should I put these six parameters - "corMhapSensitivity=high", "corMaxEvidenceCoverageLocal=10", "corMaxEvidenceCoverageGlobal=10", "oeaMemory=32", "redMemory=32", "batMemory=200"?

correct
canu -correct
-p ath -d pb_ath
Threads=10 gnuplotTested=true
genomeSize=5m minReadLength=2000 minOverlapLength=500
corOutCoverage=all corMinCoverage=0
-nanopore-raw pb.fasta.gz

trim
canu -trim
-p ath -d pb_ath
maxThreads=20 gnuplotTested=true
genomeSize=5m minReadLength=2000 minOverlapLength=500
-nanopore-corrected ath/pb_ath.correctedReads.fasta.gz

assemble
canu -assemble
-p ath -d ath-erate-0.105
maxThreads=20 gnuplotTested=true
genomeSize=5m
correctedErrorRate=0.105
-nanopore-corrected atg/pb_ath.trimmedReads.fasta.gz

Best,

Bing

[skoren]

There's no harm if you pass all of them to all steps. However, the "corMhapSensitivity=high", "corMaxEvidenceCoverageLocal=10", "corMaxEvidenceCoverageGlobal=10" is needed for correction and the other three are for unitigging. There are no special options for trimming.

[B-1991-ing]

Thank you very much for your quick reply. Have a nice weekend still.