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Difficulty with obscure fungus smudge plot interpretation #256

@Artifice120

Description

@Artifice120

I have troubles understanding my smudgeplot. I have used follwing command to generate it

suffix=pacbio

mer=31

here=/lustre/isaac/scratch/madler5/blue_pandora_seq/Genome_Assembly/hifiasm/hifiasm/

low=2

fasta=/lustre/isaac/scratch/madler5/blue_pandora_seq/gDNA_pacbio_ONT/PacBio_Hifi_20250103/blue_pand_pacbio.fasta.gz

FastK -v -T45 -k${mer} -t4 -M16 -N${here}k-${mer}_${suffix}_table $fasta

smudgeplot.py hetmers -L ${low}  -t 24 -o ${mer}-${low}-ont-pacbio1-pairs --verbose k-${mer}_${suffix}_table

smudgeplot.py all -cov_min ${low} -o ${mer}-${low}-musca-run ${mer}-${low}-ont-pacbio1-pairs_text.smu

The smudges look like this:

Image

This is an obscure fungus genome with distant relations to sequenced fungus of questionable ploidy.

Here is the genomescope histogram as well at p2

Image Image

How should I understand my smudgeplot?

It is ~70% repetitive with a mix of transposons and palindromes and with only 7% busco duplication

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