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Difficulty with obscure fungus smudge plot interpretation #256
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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:
This is an obscure fungus genome with distant relations to sequenced fungus of questionable ploidy.
Here is the genomescope histogram as well at p2
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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