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Single contig self alignment - repeats #191

Closed fungal-spore closed 1 year ago

fungal-spore commented 1 year ago

Hi, I'd like to have a self-alignment for a single contig to visualize repetitive elements. I tried using duplicate fasta files, which works somewhat but there is lots of 'noise'. Is there a way to have Sibelia align to itself using a single fasta seq? Hope that makes sense! Thanks :)

fungal-spore commented 1 year ago

I figured out a way to do what I want, for future users. I made a second fasta file with only one nucleotide in it.

e.g.

place-holder A

Then I could run Sibelia -s fine contig-with-repeats.nt place-holder.nt -m 50 -o ./sibelia_output

This provided nice output of single contig with many of its repetitve sections shown.

iminkin commented 1 year ago

Hi @fungal-spore,

I am glad you figured it out. Just in case, you don't even need a placeholder, you can just run:

Sibelia -s fine contig-with-repeats.nt -m 50 -o ./sibelia_output

fungal-spore commented 1 year ago

I can't believe I didn't try that lol thanks!