C. Titus Brown
C. Titus Brown
(this is kind of a cross-repo issue, but I'm putting it here for now because code is evolving faster in charcoal than in sourmash :) it would be valuable to...
Usage: ## run and plot a nucmer comparison ``` python -m charcoal.alignplot nucmer ibd-genomes-2/ZeeviD_2015__PNP_Main_232__bin.27.fa.gz genbank_genomes/GCF_003481565.1_genomic.fna.gz -o xyz ``` ## run and plot a mashmap comparison ``` python -m charcoal.alignplot mashmap...
as of the merge of #160, charcoal now performs the following steps - 1. find candidate genomes for contamination analysis, based on sourmash shared hashes with GTDB r95 2. download...
if we find suspected contamination, it would be interesting to ask -- * does this contamination correlate in any way with the rest of the genome content, across all available...
ref #132, #125 some ideas for display! 1. response curve idea - show a graph of how much you have to remove to get rid of contamination. could fit that...
Note, merge into #150.
right now the biggest bottleneck in charcoal is `compare_taxonomy`, which does the summarization. It iterates over all of the input genomes and computes summary statistics for each one, and then...
right now we have - * stage 1 - hit list * stage 2 - clean based on hit list. with the idea that the hit list is something you...
for euk, mag decontamination.
In addition to the basic use case of examining contamination in genomes, charcoal can also be used to compare different assembly and/or binning procedures.