AGP or .assembly input?

[cjfields]

Hi, I'm wondering AGP input or .assembly input (as used for Juicebox) is planned? Essentially it would be great to have a way to incorporate tools that group together contigs (such as the output from HapHiC).

[cjfields]

Just to add context to this: additional information in the .assembly file (as well as other formats) can be used to define contigs vs scaffolds vs super-scaffolds (e.g., potential chromosomes). At the moment, as I understand it there doesn't seem to be a way to import external scaffolding information into PretextView, for example in Juicebox via the original or reviewed .assembly file, or via tools like HapHiC. Is that correct?

[cjfields]

Just to note, I see this appears to being developed in a fork by the developer. Looking forward to it!

[additive3]

Hi @cjfields

You can load an AGP in the latest version 1.0.4 but currently tied to how PretextView generates an AGP..
I'll look to see if we can adjust the code to accept any valid AGP however it would still need to have the same sequence input information as the map file.

As for .assembly format, no that won't be possible