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As I understand your project: you don't have a host to remove and you have metagenome samples. Notice there is a tutorial for atlas. And maybe a caveat is that the You can study all the parameters, but I think the config arguments you don't understand with the comments in the template are not so important.
There is a Configure section in the docs: Which should display a detailed configuration section, but doesn't correctly. You can find it here:
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Hello, I'm very new to learning bioinformatics and for a project, I've been tasked to analyze sequencing data from 12 environmental samples. These samples were enriched for various bacterial species and methanogens, but the identities of these species are mostly unknown (we're trying to get a better idea of these samples' genomes). I was wondering how I should be editing the config.yaml file that is produced, and how I can adjust the parameters in a way that would make sense for analyzing environmental bacteria and archaea samples that went through shotgun sequencing (if the parameters need to be adjusted at all, or if the default parameters should be used and that by itself is fine).
I was also wondering if I could get a general explanation for all of the parameters in the generated config.yaml file and what they mean (for example, "preprocess_minimum_base_frequency" in the quality control section, "megahit_merge_level" in the assembly section, "genome_filter_criteria" in the binning section, etc). Or maybe any literature or other resources that I could read to get a better idea of what these parameters mean. I've read the "configure atlas" portion of the metagenome-atlas documentation, but don't think I have the background information to fully understand it. Thanks!
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