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rrwick / Minipolish

A tool for Racon polishing of miniasm assemblies
GNU General Public License v3.0
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Option for pacbio CCS/HiFi reads #1

Open Kirk3gaard opened 4 years ago

Kirk3gaard commented 4 years ago

Hi Ryan Great job. Looks like yet another really cool tool solving a bunch of important problems with long reads!

I noticed that you have option for pacbio reads. However, it might be great to have an option for CCS/HiFi reads also.

Have you tried running it on graphs from CANU? Your circularisation step would be great there too at removing overlapping ends I assume.

Best regards Rasmus (I can finally skip my dirty hacks for showing circular contigs from miniasm nicely in bandage)

rrwick commented 4 years ago

What exactly would need to change for CCS reads? Just the minimap2 preset? Sorry - I have essentially no experience working with them!

And regarding Canu graphs, no it won't work. Minipolish assumes it's being run on a miniasm graph, so it will complain and quit if you give it a Canu graph. But Canu does its own consensus step, so I'm not sure if running Racon on its graphs would be necessary.

Kirk3gaard commented 4 years ago

Yeah I think Heng Li has thought this through minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio CCS genomic reads (https://github.com/lh3/minimap2) Me neither but I assume with the recent upgrades in throughput it might be gaining popularity.

Okay I just noticed that they removed the graph file in v. 1.9 anyway.

Kirk3gaard commented 4 years ago

Maybe just add the full suite of minimap2 options? It would be nice to be able to run minipolish with short reads as well :D.

jelber2 commented 4 years ago

See this pull request to add PacBio CCS/HiFi option to Minipolish https://github.com/rrwick/Minipolish/pull/7