Open yannickwurm opened 7 years ago
And to follow up @yannickwurm - Mccortex already does this (not sure if I was clear) - it allows longer range paths to be stored. What it does not have is a way to use colour 2 to improve the assembly of colour1. Anyway - best person to ask is @noporpoise
Hi @yannickwurm,
Yes this should be possible. Such information would be most useful when you already have a long contig and you are extending it. You'd need to assemble for a while to figure out which 10X genomics fragment(s) you're actually on. It might be easier to use map 10X genomics reads onto contigs for scaffolding after assembly. There was an interesting paper from Serafim Batzoglou's group on improving mapping by using 10X-style information[1].
To add the information into the graph, a multicolour approach would work but you'd need a new colour per sample which would be memory intensive. A low memory implementation could use a bloom filter to store unitig => fragment membership. It would also require a statistical model to make junction choices. I'm afraid it's not something I could do at the moment. Certainly an interesting idea though.
[1] Read clouds uncover variation in complex regions of the human genome
Hello, as discussed briefly with Zam, it would be pretty neat if cortex could handle two layers of colors: