contaminantsDb

[microsud]

Hi @schyen
If I remember correctly, we also discussed creating a database of contaminants. Are you still up for it?

• Collecting raw fastq files for negative controls from both our labs
• Running them through dada2 pipeline
• Assigning taxonomy with multiple (or one) database
• Matching them to the published list of contaminants (?)

Maybe at some later stage, we can check with other labs if they have negative controls to populate this database?
Let me know your thoughts.
cc @sfeds @nickilott

[schyen]

Hi Sudarshan,

yes! I still need to gather all our negative and positive control fastqs together but once I do, I can send them over to you. I can run your negatives (and positives) in our dada2 pipeline too.

I guess one thing we need to decide is how do we want this contaminants database to be used? Will it be a community contribution thing, like the positive control database? In that case, the framework can be similar to what we end up deciding for the positive control database.
Or will it be more for internal use? In that case, it would ok to just keep the data within the package and we update it ourselves as we accumulate more negative controls. I guess the main question is what do we want negative controls to be compared to.

Sorry that was a bit of a brainstorm, but I'd be curious to hear what others think!

[microsud]

We can for now focus on our own controls and use them. Later one we can figure out how best we can support custom databases, where each user can input their own contaminants db for analysis.