👋 Welcome to Bactopia Discussions! 👋

[rpetit3]

👋 Welcome everyone!

I've always made heavy use of Issues for Bactopia. I think its a great way to put things out there, whether it be a bug, feature request or a question. It does feel kind of awkward saying everything is an Issue.

So, let's give Discussions a try! Please feel free to ask questions, share your ideas, and engage others about Bactopia!

I think Discussions has a great potential and am very interested to see where it goes!

Thanks everyone!
Robert

[sudeep71]

Great pipeline:) Easy to use and works well!

When calling SNPs, can you give it a local fasta ref than one it retrieves based on close match?

[rpetit3]

Thank you very much!

You certainly can provide your own reference genome. I need to update the docs because currently its kind of hidden. But bactopia datasets has a --reference option:

  --reference STR       A reference genome (FASTA/GenBank (preferred)) file or
                        directory to be added to the optional folder for
                        variant calling. Requires a single species
                        (--species).

This option will put a given reference genome in the correct directory for you. So for example if you had a Staphylococcus aureus reference, you would do the following:

bactopia datasets --outdir /path/to/datasets --species "Staphylococcus aureus" --reference USA300.gbk

Then when you ran Bactopia with --datasets /path/to/datasets --species "Staphylococcus aureus" it would recognize USA300.gbk and call variants against it.

[gshgit]

Hi Robert, I try this command but it seems that nothing changes in my datasets folder.

My code is:
bactopia datasets --outdir /mypath/datasets --species "Pseudomonas aeruginosa" --reference myRef.gbk

I checked the folder for reference genomes (I think it is /datasets/species-specific/pseudomonas-aeruginosa/optional/reference-genomes) and it is still empty.

I also checked the command output and didn't find what it did to my reference genome file 'myRef.gbk'.

Have I missed anything in the command?

Here is the command output:

root:INFO - Pseudomonas aeruginosa verified in ENA Taxonomy database
root:INFO - Setting up Ariba datasets      
root:INFO - vfdb_core (/mypath/datasets/ariba/vfdb_core) exists, skipping     
root:INFO - card (/mypath/datasets/ariba/card) exists, skipping    
root:INFO - Setting up pre-computed Genbank/Refseq minmer datasets   
root:INFO - /mypath/datasets/minmer/genbank-k21.json.gz exists, skipping   
root:INFO - /mypath/datasets/minmer/genbank-k31.json.gz exists, skipping   
root:INFO - /mypath/datasets/minmer/genbank-k51.json.gz exists, skipping   
root:INFO - /mypath/datasets/minmer/refseq-k21-s1000.msh exists, skipping   
root:INFO - Setting up pre-computed PLSDB (plasmids) datasets   
root:INFO - /mypath/datasets/plasmid exists, skipping   
root:INFO - Setting up antimicrobial resistance datasets   
root:INFO - Setting up latest AMRFinder+ database   
root:INFO - AMRFinder+ database saved to /mypath/datasets/antimicrobial-resistance/amrfinderdb.tar.gz
root:INFO - Setting up MLST datasets
root:INFO - Pseudomonas aeruginosa MLST Schema (/mypath/datasets/species-specific/pseudomonas-aeruginosa/mlst/default) exists, skipping
root:INFO - Setting up custom Prokka proteins
root:INFO - /mypath/datasets/species-specific/pseudomonas-aeruginosa/annotation exists, skipping
root:INFO - Writing summary of available datasets

[rpetit3]

Hi @gshgit,

I'm going to look into this. It looks like you've done everything correctly

[sudeep71]

Prefect! i will give it a try!

…

On Thu, Dec 17, 2020 at 4:50 PM Robert A. Petit III < ***@***.***> wrote: Thank you very much! You certainly can provide your own reference genome. I need to update the docs because currently its kind of hidden. But bactopia datasets has a --reference option: --reference STR A reference genome (FASTA/GenBank (preferred)) file or directory to be added to the optional folder for variant calling. Requires a single species (--species). This option will put a given reference genome in the correct directory for you. So for example if you had a *Staphylococcus aureus* reference, you would do the following: bactopia datasets --outdir /path/to/datasets --species "Staphylococcus aureus" --reference USA300.gbk Then when you ran Bactopia with --datasets /path/to/datasets --species "Staphylococcus aureus" it would recognize USA300.gbk and call variants against it. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#163 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABTRXKDD4FBSOBBJUBC5JR3SVJ4JLANCNFSM4USXKCEQ> .