Hello,
I have old illumina genomes that I would like to improve with a scaffolding step.
For scaffolding I have long reads (pacbio or nanopore depending on species).
Do you have any softwares recommendation to do that ?
Thank you.
My go to tool is LINKS (from the ABySS assembler team). works fine and is quite performant. Will not do gap-filling with the long reads though (can recommend racon for that step)
I think you meant PBJelly (https://sourceforge.net/projects/pb-jelly/) or LRGapcloser (https://github.com/CAFS-bioinformatics/LR_Gapcloser) for gap closing instead of racon (as far as I know it's meant for polishing)
No, (though the two you mention also do that but much less efficient and slower), I did mean racon.
it does both polishing and gapfilling.
(would never advise anybody to get involved with PBJelly, at least not if your genome is above a few Mb size, it will take for ever if you ever get it to run in the fist place)
My apologies - I actually didn't realize that Racon would fill gaps if reads span gaps in the original assembly (https://github.com/isovic/racon/issues/84)
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version 2.3.6
Did you try looking for something yourself (google or here on biostar)? It's always appreciated to see that people at least tried to get a solution themself