Hi,
I have a very fragmented reference genome https://www.g3journal.org/content/9/7/2039 samtool generate a huge fai index file of 1.35gb, which is way too big to load into Jbrowse2.
How can i "simplify" the fasta or the fai file? what tools could i use?
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setschmann •
One might say that there is no point in loading a genome with 37 million contigs into a browser, many of the expected GUI widgets would be inoperable,
for example, the graphical dropdown widget to select chromosomes would now have 37 million entries ...
instead, select a few dozen of interesting contigs where it would make sense to look at the genome and visualize those.
okay, but i would need to import it as a reference genome, a few contigs wouldnt be enough...
make yourself a smaller reference genome, just the contigs you are interested in
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The index file is 1.35G? That seems really odd. What was the exact command you used to generate the index?
the problem is the genome is very fragemented:
those are the quast results:
From Istvan's reply and yours, it looks like you're doing things right. Like he says, a graphical tool might not work best for your requirement. See if you can either work with a different tool or tweak your requirement.
il try to remove contigs with less than 1000bp and see how it goes
That's still a million contigs. Genome Browsers are built to deal with contigs that number in the 10s (<50) typically. I hope this subset works out for you.
You could try scaffolding if it has a close relative with a more contiguous assembly. Would help reduce the number of contigs