hsnguyen/assembly

Streaming assembly for MinION data

assembly's Issues

Nanopore only mode?

Hi there, this looks like a really cool piece of software and it is doing a lot of the things we have thinking about needing to get to do real-time AMR detection from ONT runs. I was wondering if you had thought about doing a met-flye (or spades) from the first 10000 or so reads (as the seed) and then kick off the streaming mode from there? This would allow you to not need any pre loaded data (I think).

P.S. it would be really nice if the software could run smoothly on GPU enabled ARM devices so that basecalling can run in parallel to the assembly. (this is what we've been thinking about in terms of truly real-time standalone for clinical purposes: https://github.com/sirselim/jetson_nanopore_sequencing)