Depends on deprecated software (Celera, Sprai)

aubombarely / Organelle_PBA

A software to assemble chloroplast and mitochodrial genomes using PacBio data

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Depends on deprecated software (Celera, Sprai) #16

Open Neato-Nick opened 5 years ago

Neato-Nick commented 5 years ago

Hi,

I'm working on installing the dependencies, and noticed that WGS-assembler has a big notice on their website that users should be using Canu instead of WGS-assembler (Celera). Could I substitute the WGS-assembler commands for Canu without breaking much? http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page

The other issue is Sprai. That appears to depend on Celera as well. Are there plans to change this for a different assembler?

diriano commented 5 years ago

I suggest using https://github.com/rrwick/Unicycler, I have had success assemblying plant mitochondrial and plastid

Neato-Nick commented 5 years ago

@diriano looks like a nice tool, I'll check it out. Thanks!

kimnegrette3 commented 4 years ago

Hi @aubombarely! Are there any updates on this issue? is the pipeline still using WGS or you may give any suggestions on using Canu within Organelle_PBA? Thanks!