Hello,
I recently received metagenomic 16S rRNA gene sequence data from a company, which includes both raw reads, and clean data with barcodes removed. My goal is to analyze these sequences and obtain information on the taxonomic diversity and abundance of the species present in the sample.
Since I use a Windows system and cannot utilize Mac or Linux, I would greatly appreciate guidance on how to proceed with this analysis. Are there any web server-based applications available that can assist with this task?
Furthermore, if there are any researchers or experts interested in this project, I would be grateful to explore potential collaborations. Please feel free to reach out to me if you are interested or have any recommendations.
Thank you in advance for your assistance.
Best regards
Looks like Qiime2 can be a good choice to start with. It can be install in Windows through WSL:
https://docs.qiime2.org/2023.5/
Another option that can be implemented online is microbiome analyst pipeline:
https://www.microbiomeanalyst.ca/
Also you can conduct taxonomic classifications with Mothur algorithm, wich uses SILVA and some other databases. It also can be installed in windows and you can follow some analysis examples in their website:
https://mothur.org/
Hello!
If you are comfortable with R, you can also try to use DADA2 (https://benjjneb.github.io/dada2/). It's an easy pipeline to get ASVs and assign taxonomy. Plus, there is a way to use the pipeline's output in phyloseq for microbiome analyses.
I personally used DECIPHER before (http://www2.decipher.codes/index.html). The algorithm for taxonomic assignation is a bit faster if you have a large dataset.
I think you can explore and try EasyAmplicon (EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research), although I haven't used it for similar analysis. As its name implies, it may be able to help you solve your problem and there is a lot of help material you can look up to use. Finally, if you do need help, I'm happy to help.
Hi, our lab members have used MOTHUR to analyze the amplicon data. The team members of mothur are extremely active and give you instant feedbacks on your work problems. You can check these papers for reference:
Article Uncovering the hidden bacterial ghost communities of yeast a...
SilvaNGS - simple and win-based. https://ngs.arb-silva.de/silvangs/ It is probably less flexible than all nice approaches mentioned above but it is quite useful for first look or for someone who needs an established reliable pipeline
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