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Hi everyone! Would you consider including the foll...
# funcscan
o
Hi everyone! Would you consider including the following tools in the pipeline: Traitar, MacSyFinder, ISEScan, geNomad, dbCAN, and CarveMe? I’ve already developed modules for Traitar and MacSyFinder; dbCAN and geNomad are already available as nf-core modules. CarveMe and ISEScan are on my to-do list for development.
j
dbCAN is already in! See dev branch, you can you summarise what rest of the other tools are used for?
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o
Tritar- phenotype prediction, MacSyFinder - Detection of macromolecular systems (CRISPR-Cas, Type IV-filament, Bacterial secretion, conjugative, decayed conjugative and mobilisable elements), ISEScan - identification of insertion elements, genomad - identification of mobile genetic elements, carveme - genome-scale metabolic model reconstruction
a
geNomad is available in #CE9MS66BS and it was also planned for #C05E9C2B2BG, but the latter never made it to a 1.0.0 release
o
ok, but what if I work with isolate and want to check it with geNomad?
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j
Hrmm, we need to make sure that #C02K5GX2W93 doesn't turn into a spaghetti screening for anything. It's not designed to be a swiss army knife for every form of microbial features.. I guess a good rule of thumb is we would want to have at least two tools that screen for the same feature
Someone else has asked about CRISPR-CAS9 screening though, so that would be a good fit
If we find another tool that does it
geNomad is a bit of a grey area
From what I remember at a bit reluctant
(sorry slow reply, currently with son who is home fro . kindergarten today)
a
CarveMe could be a great addition to the pipeline, IMO. And if we want an alternative, a popular one would be gapseq, which is available in Bioconda: https://anaconda.org/channels/bioconda/packages/gapseq/overview
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o
Are there better tools compared to genomad to screen for viruses?
oh, no. Gapseq is blast-based . It is very slow 🫠
a
gapseq can use diamond/mmseqs2 instead of blast.
j
Are there better tools compared to genomad to screen for viruses?
Yeah, that's my point @Olga Brovkina - we are not trying to be a taxonomic classifier pipeline. Really we should have someone resurrect the phage annotator pipeline, like @Alexandru Mizeranschi said
o
Hi @James Fellows Yates, thanks for the feedback! I understand the concern about keeping funcscan focused. Let me reframe my proposal around your "two tools" principle. We can couple MacSyFinder, which screens for multiple functional systems with ISEScan and we'd have comprehensive MGE profiling. Probably geNomad can also compliment this analysis. CarveMe + gapseq would be nice for available alternatives for metabolic reconstruction.
Regarding Traitar - could we pair it with PanPhlAn3(phenotype/metabolism prediction)? Or is phenotype prediction conceptually outside funcscan's scope?
j
Hrmmm, I think these are all still falling out of scope
Isn't MacSyFinder looking for multiple different features?
And metabolic reconstruction is also out of scope (IMO), as they are not loooking for specific genes types - metabolic reconstruction to me sounds like tertiary analysis
What do you think @Jasmin Frangenberg?
I sort of feel all of these may warrant a standadlone pipeline
o
This sounds great to me. Shall we discuss this possibility on next metaomics meeting? I can prepare a draft concept 😇
j
Sure!
@Daniel Lundin FYI for teh agenda 🙂
d
Perfect
j
I'm late to the party 😬 But thank you for proposing the tools for MGE profiling and metabelic reconstruction. MGE tools might me useful in funcscan (useful to know where the predicted AMPs/ARGs/BGCs come from). But I agree to outsource this functionality into a separate pipeline since it's not really a "gene function". So yes, let's discuss in the next meeting!
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