Arang Rhie

Hello, you get +inf when there are no error kmers found. If you are using HiFi kmers to evaluate an HiFi assembly, this could happen. If you have Illumina reads,...

@HaoWangLYL , sorry I missed your next question! QV isn't affected by the extra stuff in the read kmer db. Bacterial pollution / mitochondria / chloroplasts may be observed as...

Hi Ben, Glad to hear that merqury is being useful! ## 1. Collect all k-mers in your assembly ``` meryl count k=$k asm1.fasta output asm1.meryl # If you have 2...

Forgot to add the `-c` in pigz. Fixed in my above comment. Feel free to come back in case there are any other errors. Will leave this issue open so...

Hi Ben, Sorry for the delayed reply. You can set `-memory` option in meryl-lookup. For your example, you could use `-memory 20` which will limit to use at maximum 20G....

I think that's a fair strategy. I'd have done the same thing. From the histogram (`meryl histogram read.0.meryl`), I'll pick the multiplicity N (first col) which has the minimum count...

Hello @kneubehl , it seems like your meryl is not updated, or used from the previous path. Could you double check this is the path where v1.3 was installed?

Alex, this is the help message for meryl-lookup in v1.3: ``` usage: ./meryl-lookup \ -sequence [] \ -output [] \ -mers [] [...] [-estimate] \ -labels [] [...] Compare kmers...

Also please use [this script](https://github.com/marbl/merqury/blob/master/trio/exclude_reads.sh) for excluding reads having kmers from a given kmer db. The syntax is: ``` meryl-lookup -exclude -sequence $read1 $read2 -mers $meryl -output ${out_1} ${out_2} ```...

Hello @yzJiang9, If you are looking for gene annotations, currently, it is only available through the [CHM13 UCSC browser](http://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_2395475_t2t-chm13-v1.1). All raw data of each tracks can be downloaded from [here](https://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.1/)....