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k-mer based assembly evaluation
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asm.st.png vs asm.fl.png plot #59

Closed B10inform closed 2 years ago

B10inform commented 2 years ago

Hi,

What are the asm.st.png and asm.fl.png plot. The asm.st.png looks bit off, portion of the peak is out of the range.

Is it possible to get "CONTINUITY and PHASED" blocks for the haplotype resolved genome (diploid genome with two phased haplotypes)?

spectra-asm.st.png image

spectra-asm.fl.png image

This is spectra-cn.st.png image

hap1-spectra-cn.st.png (hap2 looks same) image

Thank you

arangrhie commented 2 years ago

Helo @B10inform ,

The .st.png are stacked, filled version of the histograms, while .fl.png contain unstacked, filled histograms. The .ln.png contains the line version only, identical to .fl.png, without the filled color.

arangrhie commented 2 years ago

Yes, it is possible to have shared peak smaller than the hap1 hap2 peak. This happens if the genome contains very diverse haplotypes.

For obtaining phase block related statistics and plots, you'd want to run Merqury in trio mode with haplotype specific kmers (hapmers). More details are laid out here: https://github.com/marbl/merqury/wiki#3-phasing-assessment-with-hap-mers-details

B10inform commented 2 years ago

Hi Arang

merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl athal_COL.fasta athal_CVI.fasta test-2

how were the .meryl file created. Were they created using the following files? F1.k18.meryl - reads.fastq col0.hapmer.meryl(mat) - COL.fasta cvi0.hapmer.meryl (pat) - CVI.fasta

Thanks

arangrhie commented 2 years ago

Hi @B10inform ,

The hapmers were created using the original parental assemblies from the FALCON-Unzip paper. No read data were available.

COL.fasta and CVI.fasta were generated with TrioCanu.

Arang