[feature request] - add assembly accession support to bactopia search

[tfischer78]

Hello, I'm trying to use genomes from public databases and having a problem. The sequence I'm analyzing starts "SRR" and the program gives me an error saying it needs "SRX*".

I've truncated the accessions below

bactopia \ --accession SRR101**

Similar problem when I call a assembly and bioproject.

bactopia-search -q PRJNA**

The bioproject gives a warning that there are no reads in ENA, but it is from NCBI.

bactopia \ --accession DALQ**

[rpetit3]

Hi @tfischer78,

Thank you letting me know of this issue. Could you by chance share the full accession so I can get a fix put in place for you?

Cheers,
Robert

[tfischer78]

Thanks Robert! So nice to hear from you. These were the sequences I was testing: bactopia-search -q PRJNA514245 bactopia \ --accession SRR10177533 bactopia \ --accession DALQDS000000000 Thanks, Tony On Feb 1, 2024, at 3:23 PM, Robert A. Petit III ***@***.***> wrote: Hi @tfischer78<https://github.com/tfischer78>, Thank you letting me know of this issue. Could you by chance share the full accession so I can get a fix put in place for you? Cheers, Robert — Reply to this email directly, view it on GitHub<#476 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BEY4IVKY4EKXR3VC4UIITZ3YRQBTTAVCNFSM6AAAAABCVTRTKCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRSGI3DSMBYHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[rpetit3]

Alright here's what I'm thinking

For accession: SRR10177533

I made it require SRX accessions because of the way the accessioning hierarchy, a single sample could have multiple runs (SRR), but only one experiment to represent the sequencing.

So, first we'll will want to use bactopia search to convert the SRR to SRX.

bactopia search --query SRR10177533
bactopia --accessions bactopia-accessions.txt

Or, for one sample I would probably just pull it from NCBI manually: SRX6899308

bactopia --accession SRX6899308

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Now for the assemblies. Unfortunately, at the moment there isn't a way to rapidly pull assembly accessions using bactopia directly. I've been thinking this would be a nice feature to add (e.g. allow assembly accessions in bactopia-search)

So for, PRJNA514245, this might be a problem (unless you already know this), but it has 300K+ assemblies associated with it. So I will avoid it for now.

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finally for, DALQDS000000000, Bactopia expects the NCBI Assembly accession (GCF_, GCA_). So you will want figure that out (spoiler, it is: GCA_027253235).

With the NCBI Assembly accession, you can then pass it to Bactopia

bactopia --accession GCA_027253235

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Hope this helps!

[rpetit3]

haha, Tony I hope you're OK with me hijacking this to turn it into a feature request!

I'll also improve the working on the "error saying it needs "SRX*" to suggest using "bactopia search"

[tfischer78]

Thanks so much! This is very helpful. I was having a hard time finding GCA numbers starting from the bio project. I see that I can get it now using ncbi.nlm.nih.gov/assembly but this page looks like it’s getting taken down. Important Update Effective May 2024, NCBI's Assembly resource will no longer be available. NCBI Assembly data can now be found on the NCBI Datasets genome pages. I appreciate the help- You are so fast and responsive! Thanks, Tony On Feb 1, 2024, at 3:48 PM, Robert A. Petit III ***@***.***> wrote: haha, Tony I hope you're OK with me hijacking this to turn it into a feature request! I'll also improve the working on the "error saying it needs "SRX*" to suggest using "bactopia search" — Reply to this email directly, view it on GitHub<#476 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BEY4IVLG5LLP3MG2QCR65R3YRQESFAVCNFSM6AAAAABCVTRTKCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRSGMYDKMRQGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[rpetit3]

I noticed that disclaimer as well. I'm hoping once it goes through it was be an automatic change (e.g. an Assembly accession takes you straight to Datasets)