C. Titus Brown
C. Titus Brown
would be nice to have a detailed explanation of each figure, with some examples; and then link them directly into the notebooks.
with the latest release, we're getting errors like this when running `summarize_mapping`: ``` rule make_combined_info_csv_wc: input: output: outputs.gut-viruses/gather/p8808mo11.genomes.info.csv jobid: 11 wildcards: sample=p8808mo11 resources: tmpdir=/tmp error: file outputs.gut-viruses/genomes/.genomes.p8808mo11 is empty!? ```...
right now we have `defaults.conf` and `system.conf` in the `genome_grist/conf` directory, and then a project specific config. It might be nice to support a cwd-specific configuraton file, like `system.conf` or...
So @taylorreiter gave me some internally sequenced and processed files that I wanted to feed into genome-grist, and I wrote the following little Snakefile to bypass all of the SRA...
the bug I fixed in https://github.com/dib-lab/genome-grist/pull/87 is something that I would like to make sure never happens again. so I think it's time to move a lot of the mangling...
it would seem to make sense to have the sgc queries be done on pangenomes at the species or genus level, rather than individual genomes. we could accomplish this by...
This PR explores the prefetch results (containing all overlapping genomes), as a way of beginning to evaluate strain specificity of the minimum metagenome cover. Specifically, * adds a target `map_prefetch`...
see https://github.com/sourmash-bio/sourmash/issues/1841 - should we provide an explicit config setup in grist to allow for filtration based on either estimated ANI or min k-mer coverage of genome, to allow for...
This modification adjusts copy_local_genomes to take in one file with many genomes - useful for a phage or viral database, for example. Located on farm in `/group/ctbrowngrp/scratch/ctbrown/gut-phage-db.grist/copy_local_genomes.py`. ``` % diff...
turns out I was assuming a few different weird things about identifiers in different places. The few things I've found in the process of fixing a bug reported by e-mail...