Adding GetOrganelle

[erinyoung]

Adding GetOrganelle

[Midnighter]

Given that this is the first time we see this request, maybe it'd make sense for @erinyoung to adapt the taxprofiler pipeline for their purposes as a proof-of-concept, and then we decide if/how to adopt it?

[jfy133]

Hmmm, that's an interesting one. It half fits the scope, but I'm a little wary of the assembly bit. @nf-core/taxprofiler what do you think? (and @maxibor ?)

[sofstam]

I am not sure into what category this tool would fall into. It seems a bit specific to me and agree regarding the assembly part.

[jfy133]

So to me basically it:

• Assembles as many organelle genomes as possible to get long contiguous sequences
• Tries to identify which species the organelle comes from by comparing to a set of mt database

I think conceptually this would actually fit. Just rather than short-read alignment or kmer-comparison, it does 'long-read' comparison to a database (the main difference is that it generates the 'long reads' itself).

[jfy133]

Given that this is the first time we see this request, maybe it'd make sense for @erinyoung to adapt the taxprofiler pipeline for their purposes as a proof-of-concept, and then we decide if/how to adopt it?

What do you mean by PoC - as in make a fork, add it, and see if it makes sense?

I think conceptually it does what we want (I just need to check the output), it's just outside our typical direct kmer/alignment of reads concept

[jfy133]

I just had a quick look: @erinyoung does the tool at all produce a OTU/taxon like table as output at all? I tried to look through and couldn't find anything like that. The closest thing to a table was listing gene loci rather than species

[Midnighter]

What do you mean by PoC - as in make a fork, add it, and see if it makes sense?

As PoC, I meant to add the modules and make data flow adjustments needed to get the pipeline to work as needed for the purpose, yes.

[erinyoung]

I created a nf-core module for getOrganelle (nf-core/modules#4484). The output is a fasta file with either complete or partial organelle/plasmidome sequences.

[jfy133]

Thanks @erinyoung !

So if the output of the module is simply fasta files, I don't consider that in scope for taxprofiler - as that means it is simply just an assembler.

However I saw there is this utility function: https://github.com/Kinggerm/GetOrganelle/wiki/Usage#summary_get_organelle_outputpy

Depending on what the output of that looks like, this may sort of make it fit.

[erinyoung]

My apologies, but I've encountered other priorities. I may get back into the issue at a later, but am closing this for now.