C. Titus Brown
C. Titus Brown
now that we have simultaneous contamination output/analysis across different levels per #128 #130, it would be nice to get some summaries of which taxa are most often contaminated at what...
there are reasons why this kind of thing wouldn't always work, but even that could be interesting. we could use Luiz's MAG search (https://blog.luizirber.org/2020/07/24/mag-results/) to see if putative contaminant contigs...
it'd be super nice to have some ways for people to dig into charcoal predictions of contamination. we can't provide it as part of the default charcoal workflow unless we...
it'd be nice if there was a way to let user notes travel with genomes, like "this is the one that had a cool function"
this would be another interesting control - SAGs are extremely unlikely to be contaminated, I would think.
with the alluvial flow diagrams, we now give enough information that people might be interested in extracting contigs from specific lineages. would be good to permit that. could also be...
``` charcoal run conf/ibd2.conf --use-conda -j 4 --config strict=0 -- output.ibd2/report/GCF_000371685.1_Clos_bolt_90B3_V1_genomic.fna.gz.fig.html ``` would work on the snakemake command line but does not in charcoal; I think it has to do...
right now, `contigs_search` outputs the length of each contig in bp, plus its gather taxonomic profile. in order to visualize or explore which contigs are invisible, we need to know...