Closed mscarbor closed 11 months ago
fpusan
commented
1 year ago You can assign taxonomy to long reads with SqueezeMeta (see the script in utils/sqm_longreads.pl) without assembly.
However I actually have plans on incorporatic gtdb for MAG/pangenome analysis, hopefully later this year
jtamames
commented
1 year ago Hello Matt
Thanks for being a loyal user! We would love to integrate GTDB into SqueezeMeta. For now the enormous size of the databases they are using is preventing us to do so. But I promise to rethink this issue and see if we can do it somehow. As Fernando likes to say, stay tuned.
Best,
J
On 1/3/23 21:35, Matt Scarborough wrote:
Long time user, first time poster... Thanks for all that you and your team do.
Are there any suggestion/ plans to incorporate GTDB taxonomic classifications with SqueezeMeta? As of now, it looks like a GTDB database is not available. I would love to be able to assign taxonomy to long reads with SqueezeMeta. It's a big ask, I know, but I'm throwing it out there.
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mscarbor
commented
1 year ago Javier/ Fernando-- Appreciate the quick responses! Makes sense that this would be a significant effort... Reach out if you ever need a letter from a user/PI to support the effort.
fpusan
commented
1 year ago Work towards this has started in a0ae6a7, though for now we are using it to classify bins rather than long reads. I see that you'd like to use it to classify individual long reads. Have you seen it used like that elsewhere?
mscarbor
commented
1 year ago No, actually! Since the GTDB is based on just the concatenated sequences of their marker genes, this wouldn't actually work, would it? Having it for bins would be amazing though :-)
On Mon, Sep 18, 2023 at 11:38 AM Fernando Puente-Sánchez < @.***> wrote:
Work towards this has started in a0ae6a7 https://github.com/jtamames/SqueezeMeta/commit/a0ae6a7b3f0fd12af9b1b07b581aef431d747494, though for now we are using it to classify bins rather than long reads. I see that you'd like to use it to classify individual long reads. Have you seen it used like that elsewhere?
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fpusan
commented
11 months ago Just found this again and though a bit more about it.
It may be cool if the reads are long enough to contain many marker genes but in practice your mileage may vary since for now PacBio reads are not that long. Also I am not sure whether the different genes have the same phylogenetic resolution (I wouldn't be surprised if they don't).
So in practice I suspect this method would work very differently for different reads (from no classification at all to super accurate classification, and a range between both, depending on the number and "power" of the marker genes contained on each read). It may still a cool idea but I don't think it is something we are going to prioritize in the near future.
GTDB-Tk for bins is however already working in our dev version! https://anaconda.org/fpusan/squeezemeta-dev
For now the GTDB-Tk results are added to the bin table as an extra column (if the --gtdbtk flag was provided in the initial SqueezeMeta.pl call. I expect this to make into an "official" release sometime in Q1 2024, once we have time to do more testing and bring all the new features to our usual levels of stability (which is to say, somewhat stable...)
fpusan
commented
11 months ago However someone else seems to be doing what you suggested... https://www.biorxiv.org/content/10.1101/2023.12.17.572079v1
mscarbor
commented
10 months ago Ok, amazing. Thanks for sharing this.
On Tue, Dec 19, 2023 at 2:47 AM Fernando Puente-Sánchez < @.***> wrote:
However someone else seems to be doing what you suggested... https://www.biorxiv.org/content/10.1101/2023.12.17.572079v1
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Long time user, first time poster... Thanks for all that you and your team do.
Are there any suggestions or plans for incorporating GTDB taxonomic classifications with SqueezeMeta? As of now, it looks like a GTDB database is not available. I would love to be able to assign taxonomy to long reads with SqueezeMeta. It's a big ask, I know, but I'm throwing it out there.