Ryan Wick

I managed to make bwa-mem2 compile on macOS 11.5, but it wasn't easy :smile: As stated above, the safestringlib was the problem. First of all, I had to use the...

Unicycler chooses the 'best' assembly using contig count and dead end count, so I see why it made the choice it did. I don't, however, understand what's going on with...

Two guesses: 1. The short read assembly graph has a very complex knot that is confounding Unicycler's path-finding algorithm. I.e. there are so many possible ways to bridge two segments,...

Unicycler builds bridges with long reads in two ways: 1. Using a miniasm assembly (what you quoted above). This takes a decent amount of long reads but doesn't rely as...

Yes, all of those things you said could be informative. I would also try aligning the assemblies to each other: [Mauve](http://darlinglab.org/mauve/mauve.html) is good if you want a GUI tool, and...

Thanks for the suggestion - I'll add it to the list :smile:

Thanks! People have requested support for custom adapters a few times, so I'll definitely have to add this feature. I'll take a look at your implementation for inspiration!

Hi Henri, The `--min_trim_size` option controls how long an alignment must be for the sequence to be trimmed, and you probably don't have to change it from the default of...

I'm sure you're right - I just haven't gotten around to it. I will though, someday. I promise! 😄 A link for my own reference in the future: http://peterdowns.com/posts/first-time-with-pypi.html

I think you've uncovered an interesting bug here! The problem stems from the fact that Porechop tries to determine whether you are using forward or reverse barcodes (different kits add...