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marbl / meryl

A genomic k-mer counter (and sequence utility) with nice features.
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Using meryl to prepare for Merqury #24

Open aureliendejode opened 3 years ago

aureliendejode commented 3 years ago

Hi,

I'd like to evaluate my assembly. I have several Illumina fastq files. For each library I have one fastq file for Forward and one for Reverse reads. What is the best way to use Meryl in the goal of using that output for Merqury: Is something like this okay: meryl count k=21 lib1_1.fastq lib1_2.fastq lib2_1.fastq lib2_2.fastq ... output Illumina.meryl

Thanks

brianwalenz commented 3 years ago

That will work.

You might want to limit memory and thread usage with memory=<limit in GB> and threads=<number of CPUs to use>. By default, it will use as much memory as it wants and all the CPUs.

aureliendejode commented 3 years ago

Thanks, I used those 2 options and it worked.