C. Titus Brown
C. Titus Brown
over in https://github.com/spacegraphcats/spacegraphcats/issues/437#issuecomment-969471862, @taylorreiter sez: >I've been using #379 to assess the accuracy of #444 (or really, just protein searches in general, which need to be accurate for #444 to...
https://twitter.com/sdeorowicz/status/1512331429031591936
With https://github.com/spacegraphcats/spacegraphcats/pull/303, it is now possible to do direct node- and dominator-abundance counting. However, this is not integrated into the standard spacegraphcats CLI, so cannot be run using `spacegraphcats run`....
Now that the [minimum metagenome covers](https://dib-lab.github.io/2020-paper-sourmash-gather/) paper is reasonably baked, I've been thinking about next steps towards strain-resolved metagenome decomposition. ## reference dependence is a problem A big (the big?)...
Tackles https://github.com/spacegraphcats/spacegraphcats/issues/448. This PR extends the translated-multifasta-annotation approach added in #444 with optional 'sourmash gather'-style behavior that chooses a _minimum_ set cover of matches for each node or neighborhood. The...
https://arxiv.org/abs/2112.11696 RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning Hansheng Xue, Vijini Mallawaarachchi, Yujia Zhang, Vaibhav Rajan, Yu Lin Mixed communities of organisms are found in many environments (from the...
does it work properly?
This is a maintenance/ongoing branch for spacegraphcats v1.x. see `latest` for the latest development branch, which is being released as v2.x. This branch/PR is mostly for @taylorreiter who needs some...
## purpose I've been idly musing that there are situations where simply being able to retrieve contigs and/or reads based on k-mer queries into the cDBG would be useful. This...
from [this hackmd](https://hackmd.io/IZNaQM4lToKMLhSa9AH9cg), written for @drtamermansour :) check out https://github.com/spacegraphcats/spacegraphcats/pull/303 catlas objected loaded [here](https://github.com/spacegraphcats/spacegraphcats/pull/303/files#diff-9eb91c31cfeeac0c813cd09582309a53bfe02cd77cace354e7332740dea97d23R34) catlas root node contains components underneath - see [`catlas.children[catlas.root]`](https://github.com/spacegraphcats/spacegraphcats/pull/303/files#diff-9eb91c31cfeeac0c813cd09582309a53bfe02cd77cace354e7332740dea97d23R43) note that the k-mer sizes of each...