By Angus Ball

Introduction

Sometimes life suchs and this has been a multiday effort in sucking. I dont like qiime2's file structure and neither should you, eitherway lets get this over with, we need 3 seperate files to use in qiime, a metadata file, an otu table, and a taxonomy table. Lets start simple

getting a metadata file

First you need Keemei. download this package and follow the pictures and instructions to format your metadata file.

Getting otu and taxonomy tables

then go to your linux box and download biomformat. PS. pip is a python command so you should have access but if you don't get rekt

Then in R follow this tutorial

Very painfully preparing your phyloseq object for qiime2

then bring all these folders into the linux box and run the following command

 biom convert -i OTU.txt -o OTUbiomv210.biom --table-type="OTU table" --to-hdf5

then load up qiime2

conda activate qiime2-amplicon-2024.2

and start running these commands

import your OTU table:

qiime tools import --input-path OTUbiomv210.biom --type 'FeatureTable[Frequency]' --input-format BIOMV210Format --output-path table.qza

Imported OTUbiomv210.biom as BIOMV210Format to table.qza

Import your taxa table:

qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path  tax.txt --output-path taxonomy.qza

Imported tax.txt as HeaderlessTSVTaxonomyFormat to taxonomy.qza

Import your sequence information:

qiime tools import --input-path rep-seqs.fna --type 'FeatureData[Sequence]' --output-path rep-seqs.qza

Imported rep-seqs.fna as DNASequencesDirectoryFormat to rep-seqs.qza

Import your metadata:

qiime metadata tabulate \
    --m-input-file SAM.txt \
    --o-visualization SAM.qzv

Saved Visualization to: sample-metadata.qzv

Citations

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso. GigaScience 2012, 1:7. doi:10.1186/2047-217X-1-7

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG. GigaScience. 2016;5:27. http://dx.doi.org/10.1186/s13742-016-0133-6