I am conducting bacterial diversity analysis on sediment samples using the Oxford Nanopore MinION platform for 16S sequencing. Basecalling and demultiplexing were performed using MinKNOW.
After uploading the FASTQ files to usegalaxy.org, I am following the “16S Microbial analysis with Nanopore data” GTN tutorial:
Is there a recommended protocol within Galaxy to generate OTU/ASV and taxonomy tables in BIOM, mothur, .txt, or .csv formats?
I need these files to import into the MicrobiomeAnalyst Marker Data Profiling module ( MicrobiomeAnalyst ) to conduct downstream diversity analyses, including taxonomic abundance profiling, alpha and beta diversity, and LEfSe analysis.
Attached is the example of the OTU table and taxonomy table that I wish I can get
Any guidance or assistance on resolving this issue would be greatly appreciated.
From there, each of those has a workflow template you could adjust to suit exactly what you want to do. You can also search under Workflows → Public workflows at any UseGalaxy server to find these same workflows (but without the large context). The IWC is building out the HTP versions still, and contributions would be welcome from community scientists!
Kraken-biom Create BIOM-format tables from kraken output
Try a search in the tool panel with “biom” for more examples (from Mothur) or to convert between formats starting from a tsv dataset. A search with “kraken” will bring up most for Kraken/Kraken2.
If you need to do intermediate manipulations, perhaps for the review steps, we have cheat sheets for Text Manipulations or you can also enter a notebook environment like Jupyter.
Let us know your thoughts and how this works out! Once you know your parameters, you could edit to add in the extra tools to the end of the tutorial’s base workflow.
