microsud / tools-microbiome-analysis Goto Github PK

BTW @antagomir I was wondering what would be the best way to maintain this website resource. This could also be linked to the suggestions from @TuomasBorman
microbiome/OMA#352 (comment)

Don't know if new links are added here, but I found
metaSPARSim to be a useful tool..

Hello, nice resource! My spell checker noticed a typo in your repo name "Anlaysis" vs "Analysis". Also the "View On GitHub" link on the website to this github does not work. It just goes to the homepage of the site.

Hi,

First, thanks for your excellent resources here.
The microeco package maybe also a useful tool in this topic.

Chi

Hi Sudarshan, this list is excellent! Thank you.

I've been curating my own "Control/Contamination" ref list and here I'm sending you the ones that you might add:

• Laboratory contamination over time during low-biomass sample analysis (Weyrich et al., 2019) https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13011
• Consistent and correctable bias in metagenomic sequencing experiments (McLaren et al., 2019) https://elifesciences.org/articles/46923
• Community profiling of the urinary microbiota: considerations for low-biomass samples (Karstens et al., 2018) https://www.nature.com/articles/s41585-018-0104-z
• Identification and removal of contaminating microbial DNA from PCR reagents: impact on low-biomass microbiome analyses (Stinson et al., 2018) https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/lam.13091
• Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data (Davis et al., 2018) https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0605-2
• Recognizing the reagent microbiome (de Goffau et al., 2018) https://www.nature.com/articles/s41564-018-0202-y
• Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations (Eisenhofer et al., 2018) https://www.cell.com/action/showPdf?pii=S0966-842X%2818%2930253-1
• Optimizing methods and dodging pitfalls in microbiome research (Kim et al., 2017) https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0267-5

Best,
Svetlana