Scaffolding a genome with long reads.

Question

[Picasa]

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.

[lieven.sterck]

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

Answer 1

[lieven.sterck]

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)

[jean.elbers]

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)

[lieven.sterck]

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)

[jean.elbers]

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)

[lieven.sterck]

no need to apologise, we all learn every day ;)

[Picasa]

Thanks I will take a look