add to dropdown in Taxonomic Classification

[olsonanl]

Please add another value to the Taxonomic Classification database dropdown - "RefSeq protozoan genomes"

thanks

[dawenx]

Since we were asked to hide 'the RDP and Silva options' earlier today by @jimdavis1, I wanted to double before taking any action.

[ARWattam]

I saw a demo of this yesterday and it was really nice and I think it should be included. More information is always better.

From: Dawen Xie notifications@github.com Reply-To: PATRIC3/patric3_website reply@reply.github.com Date: Thursday, April 18, 2019 at 4:14 PM To: PATRIC3/patric3_website patric3_website@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [PATRIC3/patric3_website] add to dropdown in Taxonomic Classification (#2256)

Since we were asked to hide 'the RDP and Silva options' earlier today by @jimdavis1https://github.com/jimdavis1, I wanted to double before taking any action.

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[mshukla1]

Not so fast....

We need to decide if we want to provide protozoan (and other organism databases from the list below, i.e. fungi) as a separate databases or include it as part of the default kraken database to make it comprehensive.

archaea: RefSeq complete archaeal genomes/proteins bacteria: RefSeq complete bacterial genomes/proteins plasmid: RefSeq plasmid nucleotide/protein sequences viral: RefSeq complete viral genomes/proteins human: GRCh38 human genome/proteins fungi: RefSeq complete fungal genomes/proteins plant: RefSeq complete plant genomes/proteins protozoa: RefSeq complete protozoan genomes/proteins nr: NCBI non-redundant protein database nt: NCBI non-redundant nucleotide database env_nr: NCBI non-redundant protein database with sequences from large environmental sequencing projects env_nt: NCBI non-redundant nucleotide database with sequences from large environmental sequencing projects UniVec: NCBI-supplied database of vector, adapter, linker, and primer sequences that may be contaminating sequencing projects and/or assemblies UniVec_Core: A subset of UniVec chosen to minimize false positive hits to the vector database

Having burnt our fingers with RDP and Silva, I think we need to do due diligence and play with the new databases before we make them available to users.

[mshukla1]

I like to build the new database first, try it with some of the user datasets from the workshop, and evaluate the results before deciding whether we provide separate databases or combine them into one default database.

[olsonanl]

OK. I dust my hands of all of this and leave it to you. Please follow up with Jim and with the user from the university from South Africa.

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From: Maulik Shukla notifications@github.com Sent: Friday, April 19, 2019 11:32 AM To: PATRIC3/patric3_website Cc: Olson, Robert D.; Author Subject: Re: [PATRIC3/patric3_website] add to dropdown in Taxonomic Classification (#2256)

I like to build the new database first, try it with some of the user datasets from the workshop, and evaluate the results before deciding whether we provide separate databases or combine them into one default database.

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[dawenx]

@mshukla1 any update on this? we could keep this ticket open, but i prefer to close it if we do not have active plan to support it.