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alekseyzimin / masurca

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LHE_COVERAGE parameter #29

Open TimothyStephens opened 6 years ago

TimothyStephens commented 6 years ago

Hi,

I wish to confirm that the LHE_COVERAGE parameter is the estimated coverage of long reads given to the assembler. Currently its description is difficult to interpret.

Arkhaan commented 6 years ago

Hi,

I was asking myself the same question. I will try run it with LHE_COVERAGE = 6, as we have 6x of long reads. I hope it does mean that.

alekseyzimin commented 6 years ago

LHE_COVERAGE is the maximum longest read coverage the assembler will use. If your coverage is lower than LHE_COVERAGE then all reads will be used. Otherwise, the assembler will use LHE_COVERAGE of the longest reads, discarding the rest.

kfletcher88 commented 4 years ago

Hi, On this topic has anyone done any investigations to optimize? Is there evidence that too much LHE_Coverage could be detrimental or is it a case of the more, the better? Generally is it better to remove reads below a certain length threshold? Thanks

alekseyzimin commented 4 years ago

Hi,

Too much coverage (beyond 25-30) slows down the assembly and does not bring any improvement in the final contiguity or correctness. The assembler by default uses 25x coverage by the longest reads. You can increase theis parameter if you feel that the assembler detected the genome size incorrectly. The genome size is saved in ESTIMATED_GENOME_SIZE.txt

Best, Aleksey

On Fri, Mar 6, 2020 at 11:00 AM Kyle Fletcher notifications@github.com wrote:

Hi, On this topic has anyone done any investigations to optimize? Is there evidence that too much LHE_Coverage could be detrimental or is it a case of the more, the better? Generally is it better to remove reads below a certain length threshold? Thanks

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