Exporting data and connecting with other tools

QIIME 2 offers various ways of visualizing and processing your data further, but sometimes you may want to use other tools that are not (yet) available through QIIME 2. This is, of course, possible and very easy to do: you can export your data from any QIIME 2 artifact and use it with any of your other favourite tools, as long as the underlying format is compatible. The formats that QIIME 2 supports are common and should be readable by most bioinformatics tools - most of the time, the artifacts will contain data in the original format that the underlying tool uses. Below are some examples of how you can export data from QIIME 2 and connect it with other tools.

Warning

QIIME 2 does not yet support exporting data from the cache (see below). This means that you will need to manually copy the data from the cache directory to a location where you can access it with other tools. In our examples, the cache directory is located directly in the working directory and that is where we will copy the data from. Keep in mind that you should never tamper with the files in the cache directory directly, as this may lead to broken artifacts and failed analyses.

Visualizing Kraken 2 reports with Pavian

If you have used Kraken 2 to classify your reads, you can export the resulting reports from the corresponding QIIME 2 artifact and visualize them with Pavian which will allow you to explore the taxonomic composition of your samples in an interactive way. To export the Kraken 2 reports, you can use the following commands:

Direct export

Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of the issue here.

Workaround 1: without using QIIME

UUID=$(cat ./cache/keys/kraken_reports_reads | grep 'data' | awk '{print $2}')
mkdir ./exported_reports
cp -r ./cache/data/$UUID/data/* ./exported_reports/

This will find the UUID of the reports artifact, use it to locate the data within the cache directory, create a directory for the exported data and copy the files from the cache into it.

Workaround 2: with QIIME

mosh tools cache-fetch \
    --cache ./cache \
    --key kraken_reports_reads \
    --output-path ./kraken_reports_reads.qza

mosh tools export \
    --input-path ./kraken_reports_reads.qza \
    --output-path ./exported_reports

This will first fetch the reports artifact from the cache and then export it to the exported_reports directory.

Once you got the data into the exported_reports directory, you can then use those with Pavian. To give it a quick try, navigate to Pavian’s demo site and upload the exported files.

Microbial pangenomics with Anvi’o

Another suite of tools you may be familiar with is the Anvi’o platform. One of the workflows that Anvi’o provides is the microbial pangenomics analysis, which can be used to explore the gene clusters within your samples. You could export the MAGs obtained from the binning step and use them as input to the anvi-pan-genome workflow, as described here. To export the MAGs, you can use the following command:

Direct export

Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of the issue here.

Workaround 1: without using QIIME

UUID=$(cat ./cache/keys/mags | grep 'data' | awk '{print $2}')
mkdir ./exported_mags
cp -r ./cache/data/$UUID/data/* ./exported_mags/

This will find the UUID of the MAGs artifact, use it to locate the data within the cache directory, create a directory for the exported data and copy the files from the cache into it.

Workaround 2: with QIIME

mosh tools cache-fetch \
    --cache ./cache \
    --key mags \
    --output-path ./mags.qza

mosh tools export \
    --input-path ./mags.qza \
    --output-path ./exported_mags

This will first fetch the MAGs artifact from the cache and then export it to the exported_mags directory.