Metagenomics modules discussion

[jfy133]

To talk about metagenomics integration into schema.

Field	Type	Options	Definition
profiler	string		Can be any metagenomic profiler (i.e. taxonomic, functional etc), which is primarily defined by database
database	string		Name of database
database_desc	sub_table
profile_tsv	url
reads_assigned	integer		Number of reads assigned a category by the profiler
proportion_assigned	double
command	string		Command (including parameters) used to generate profile
note	string

Subtables

Header	Field	Type	Options	Definition
database_desc	repository			NCBI, JGI, GTDK
database_desc	publication
database_desc	taxonomic_schema
database_desc	date
profiler_desc	version

Request upstream fields (dnaSequencing or library level)

Field	Type	Options	Definition
preindexing_qpcr_copies	numeric	NA	Copy number from qPCR results pre-indexing of library. Used for OTU contaminant method when comparing blanks. Also proxy for aDNA yield.

[jfy133]

This becomes a bit scary, but parameters as well? Might be overkill though in terms of complexity.

[stschiff]

I don't think we should require perfect reproducibility. Or, rather, if you want that, perhaps it's better then to link to a protocols.io recipe, or some nextflow pipe or something?

[jfy133]

Yeah exactly. Something for us to consider the most efficient method. Maybe just including a note say check this article for parameters, would be sufficient.

Standardisation is something we want to push for though in our work as we are scaling up too, though which is why I'm bringing this up here. But might be for a different discussion elsewhere :👍

[maxibor]

One of the idea could be to run every sample through the same processing pipeline (nf-core/eager) since we wrote it to give both genomics and metagenomics results.

[jfy133]

That is something we should definitely do. However it sounds like Pop-gen will be running the internal pipeline, so something to discuss with them.

However for the schema itself we should be careful that it's very generic that groups who don't use nf-core/eager can also add stuff. Also over time different profilers outside Kraken(and sort of MALT) can be used.

Could just have a field that needs to contain the command used for the taxonomic profiler?

Another question if we should restrict to taxonomic profiling or also allow any profiler e.g. humann2 and functional stuff?

[alexhbnr]

I think we can keep it generic because in the end all of these tools are profilers of some kind and only the reference database determines whether you have taxa, functional pathways etc. Therefore, if we keep it generic, we can save us some hassle in the future in case some new tool is released.

[jfy133]

So minimum fields:

• profiler
• database
• tsv_file for output?

Any other useful metadata? Number of reads assigned, for example?

Another question is are we integrating this into 'sequencingDna' or a separate module? We will need to check phrasing that it doesn't overlap nad is distinct from the pop-gen fields.

I will make a table in the OP to keep track?

[maxibor]

Hmm,
In curatedMetagenomicData, they chose to go only for Metaphlan2

[alexhbnr]

I think these minimum fields plus the number of assigned reads should be fine.

I would not put it into sequencingDna because the results of the profiling are related to 'sequencingDNA' but you could have multiple profiles per sequencing run, one for each profiler. I would only keep the information about the reads aligning to the host genome in sequenceDna.

Regarding curatedMetagenomicData, we don't have to restrict ourselves as long as we agreed on a standard database of the profiler.

[jfy133]

Sure. We can still internally have our standards, and ship all our modules accordingly, but I don't think the Stephan's idea of this framework is to force particular standards on people. It is just meant to be a consistent way of reporting metadata.

[jfy133]

I think these minimum fields plus the number of assigned reads should be fine.

I would not put it into sequencingDna because the results of the profiling are related to 'sequencingDNA' but you could have multiple profiles per sequencing run, one for each profiler. I would only keep the information about the reads aligning to the host genome in sequenceDna.

Regarding curatedMetagenomicData, we don't have to restrict ourselves as long as we agreed on a standard database of the profiler.

@stschiff how do you think this would then work with the current title of sequencingData?