Ryan Wick

I suspect this is a limitation of Porechop's somewhat simplistic design: it currently loads all reads into memory and then processes them. So if you have more reads than you...

Thanks - this has given me lots to think about 🤔 ### Automatically choosing a threshold For finding an 'optimal' threshold, I suspect that a simple rule (e.g. 95%) might...

Hi Juan, Something has clearly gone wrong in during assembly or polishing: the input file to Racon seems to have a total size of 0 bp. I'm not sure where...

That's a tough one, and I don't know why you're getting the discrepancy. It will probably take some experimentation and detective work! Some miscellaneous thoughts: * You're using a _C....

It seems that Minipolish is having issues getting reads from its temporary file. Maybe you don't have read/write permissions for `/tmp` or something like that? You could try setting your...

Hi Ryley, While the read identity will affect minimap2 alignments, I wouldn't expect the error model (e.g. pacbio2016 vs nanopore2020) to make too much of a difference. What exactly do...

That's a good point, so thanks for that suggestion. I don't think I'll build this feature into Polypolish itself, but it could be implemented in a separate script using Polypolish's...

Hi Florencia, I'm curious is this is a problem with the miniasm assembly or with the Minipolish polishing. Does the miniasm assembly graph (i.e. before running Minipolish) contain 6 unconnected...

Hello! I ran into this same issue (also on WSL + Ubuntu), and I came up with a different workaround. Since the problem seems to be that `mamba create --force`...