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jkimlab / RBRC

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The assembly genome is still fragmented #1

Open 444thLiao opened 1 year ago

444thLiao commented 1 year ago

Thank you for your efforts. I recently obtained over 30 NGS data sets that are all closely related to one another. We obtained over 500 contigs for each genome after denovo reference-free assembly.

Then, using the nanopore platform, we attempt to sequence ten of them and obtain nearly complete genomes.

To save money, we intend to use the nanopore sequencing as a guide for assembling the remaining 20 genomes. I still got over 500 contigs per genome using the default parameters of your pipelines. Do you have any suggestions for improving the assembly results?

Attached here is one of the log.

log.PROGRESS.txt

jkimlab commented 1 year ago

Thanks a lot for your interest in RBRC. I think that it could be helpful to use a lower resolution value. Please try to change resolution option to 50K or 100K.

Additionally, I suggest using PLR-GEN, which is our another tool for generating longer sequences. PLR-GEN is a tool for metagenome assembly, but I think it could be helpful for your data and used references.