C. Titus Brown
C. Titus Brown
- [ ] Run https://github.com/spacegraphcats/spacegraphcats-dory-example - [ ] Run https://github.com/spacegraphcats/spacegraphcats-twofoo-example
per http://ivory.idyll.org/blog/2021-transition-to-pyproject.toml-example.html Motivated in part by https://github.com/spacegraphcats/spacegraphcats/pull/407, where I updated the various requirements files and discovered that we have redundant and sometimes disagreeing requirements in `environment.yml`, `requirements.txt`, and `setup.py`...
related to updating contributors https://github.com/spacegraphcats/spacegraphcats/issues/398, I think we should consider submitting the v2 release in [the Journal of Open Source Software](https://joss.theoj.org/).
we should add @mogproject to list of contributors!
I've merged #233 in the interests of getting on with life, but there are a few issues that need to be added to robustify it: - [x] the extract_reads_for_hashvals rule...
The annotation approach added in #282 seems to be working out pretty well, and I had a few thoughts about how to extend and/or regularize it, as well as how...
for @drtamermansour: Snakefile rule to make random-access gz file (bgzf): [link](https://github.com/spacegraphcats/spacegraphcats/blob/master/spacegraphcats/conf/Snakefile#L142) and [make_bgzf script](https://github.com/spacegraphcats/spacegraphcats/blob/master/spacegraphcats/utils/make_bgzf.py) Snakefile rule to build a database labeling the reads from the bgzf with unitig ID: [link](https://github.com/spacegraphcats/spacegraphcats/blob/master/spacegraphcats/conf/Snakefile#L152)...
# spacegraphcats read indexing with sgc, we need to be able to go from k-mer to cDBG unitig to read. How is this implemented? First, we put all of the...
Here's a tutorial from @taylorreiter !! # Visualizing spacegraphcats results with Bandage [Bandage](https://rrwick.github.io/Bandage/) is a useful tool for visualization of de bruijn graphs. An example of Bandage visualization that appeared...
https://hackmd.io/@ctb/BkDE7msPv