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marbl / merqury

k-mer based assembly evaluation
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Completeness, Switch Error？ #126

Open DayTimeMouse opened 1 month ago

DayTimeMouse commented 1 month ago

1716898870793

Hi,

What should the completeness in the picture be? Furthermore, what is the meaning of "all" ? Lastly, does the "2" mentioned in the picture refer to a Switch Error?

I used hifi reads to generate hifi.meryl, mat.meryl and pat.meryl are the part of hifi.meryl(used hifi_mat/pat.fastq.gz to generate mat/pat.meryl).

The command: $MERQURY/merqury.sh hifi.meryl mat.meryl pat.meryl hap1.fasta hap2.fasta phasing

Best regards.

arangrhie commented 1 month ago

Hello @DayTimeMouse,

Each column represents:

  1. Assembly
  2. k-mer set used for measuring completeness (all = read set, hap = hap-mers)
  3. Solid k-mers found in the assembly
  4. Total solid k-mers in the read set
  5. Completeness (%)

Please refer to the wiki page, especially the 3. Phasing part. Looks like your hapmer sets are larger than the read set, which is impossible by definition. The hapmers needs to be computed with parental and child k-mers.