How to get the OTU table using the accession number?

12 May 2023 1 2K Report

I am currently collecting the data for 16S rRNA sequence.

Hello!

To obtain OTU table, one will need to download raw reads (usually in a fastq.gz format) by accession number. If files are multiplexed - demultiplex first and then recreate OTU or ASV tables.

There are several pipelines that can help with it, such as Qiime2 and Mothur.

In qiime2, there is additional plugin q2-fondue (https://library.qiime2.org/plugins/q2-fondue/41/), which can help with obtaining data from repositories by accession numbers.

Good luck with your analyses.

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