C. Titus Brown

icon indicating a website link http://ivory.idyll.org/blog/ icon indicating an email [email protected]

icon company University of California, Davis icon location Davis, CA icon location Prof at UC Davis. Blogs at http://ivory.idyll.org/blog/ and uses bluesky under ctitusbrown.

Results 624 issues of C. Titus Brown

Is there any way to get the connectivity information when using cuttlefish 2?

My reading of the documentation, along with some playing around, suggests that there is no way currently get information about which unitigs connect to which unitigs when running cuttlefish v2....

how to link in the big/slow files

``` ln -s $(pwd)/outputs.one/{raw,trim,sigs,sra} outputs.one.pp ```

speed up custom genome stuff

"Loaded info on 11413 local genomes." is taking a long time... maybe time for polars/parquet?

WIP: improve output during summarize mapping step

upgrade documentation

* new GTDB version * don't use sourmash index

fix default conf.yml

should contain 'samples' instead of 'sample', if nothing else...

add various tax displays: taxburst, sankey, treemap

distinguish between `-j` and `-c` on `__main__`/command line

trap CTRL-C and run `snakemake --unlock`

...or the equivalent Python code...

ideas for grist improvements/additions - brainstorming

grist ideas - * sample comparisons * betterplot integration perhaps singleM integration?