assembly mode2 with "corrected" reads instead of assembly mode 3?

paoloshasta / shasta

De novo assembly from Oxford Nanopore reads.

https://paoloshasta.github.io/shasta/

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assembly mode2 with "corrected" reads instead of assembly mode 3? #32

Closed jelber2 closed 3 weeks ago

jelber2 commented 3 months ago

Hi, I was wondering if there might be a recommendation on using herro corrected reads with assembly mode 2, as opposed to just blindly using config Nanopore-Phased-R10-Fast-Nov2022 and --Kmers.k 30 (which seems to be used with Nanopore-ncm23-May2024), and maybe report back. I tried these reads with Nanopore-ncm23-May2024 and seemed to get good results, but I was curious about getting a haploid assembly that comes along with Nanopore-Phased-R10-Fast-Nov2022 too.

paoloshasta commented 3 months ago

We are working on assembly configurations for phased assembly with the latest ONT reads as per ONT's May 2024 announcements. We plan to release assembly configurations for both raw reads and Herro-corrected reads. These will use the new Shasta Mode 3 assembly, not Mode 2 assembly. The combination of longer and more accurate reads with new assembly methods in Mode 3 assembly will deliver assemblies with significant improvements in accuracy, contiguity, and completeness. Assembly performance (speed) will not change significantly. I cannot make any promises regarding timing but I hope it will be soon.

jelber2 commented 2 months ago

I guess you just pushed those assembly configurations with b370f1c?

paoloshasta commented 2 months ago

We hope to release 0.13.0 today. There will also be a brief presentation summarizing results.

paoloshasta commented 2 months ago

We released Shasta 0.13.0 today. See the release notes and these slides.