Kalamari

Synopsis

Kalamari is a database of completed and public assemblies, backed by trusted institutions. These assemblies can be further used in formatted databases such as Kraken or Blast.

Prerequisites & Recommendations

Requirements:

• clone this repo locally git clone https://github.com/lskatz/Kalamari.git
• NCBI entrez-utilities set of tools edirect, esearch, etc.
  • install via your package manager
  • debian/ubuntu: apt install ncbi-entrez-direct

Optional, but recommended:

• NCBI_API_KEY environmental variable
• EMAIL environmental variable

Ensure that you have the NCBI API key. This key associates your edirect requests with your username. Without it, edirect requests might be buggy. After obtaining an NCBI API key, add it to your environment with

export NCBI_API_KEY=unique_api_key_goes_here

where unique_api_key_goes_here is a unique hexadecimal number with characters from 0-9 and a-f.

You should also set your email address in the EMAIL environment variable as edirect tries to guess it, which is an error prone process. Add this variable to your environment with

export EMAIL=my@email.address

using your own email address instead of my@email.address.

Download instructions

First, build the taxonomy. The script buildTaxonomy.sh uses the diffs in Kalamari to enhance the default NCBI taxonomy. Next, filterTaxonomy.sh reduces the taxonomy files to just those found in Kalamari. filterTaxonomy.sh uses taxonkit and so this needs to be in your environment before starting.

bash bin/buildTaxonomy.sh
bash bin/filterTaxonomy.sh

To download the chromosomes and plasmids, use the .tsv files, respectively, with downloadKalamari.pl. Run downloadKalamari.pl --help for usage. However, to download the files to a standard location, please simply use downloadKalamari.sh which uses downloadKalamari.pl internally.

bash bin/downloadKalamari.pl

Database formatting instructions

How to format and query databases

Further description

Kalamari is a database of completed and public assemblies, backed by trusted institutions. Completed assemblies means that you do not have to worry about the database itself being contaminated with "rogue" contigs. Additionally, most assemblies were obtained by subject matter experts (SMEs) at Centers for Disease Control and Prevention (CDC). Those not from CDC come from other trusted institutions or projects such as FDA-ARGOS. Most genomes are from species that are either studied or are common contaminants in the Enteric Diseases Laboratory Branch (EDLB) at CDC.

Kalamari also comes with a custom taxonomy database such as defining Shigella as a subspecies of Escherichia coli or defining the four lineages of Listeria monocytogenes. These changes have been backed by trusted SMEs in EDLB.

Contributing

Please see CONTRIBUTING.md

Citation

Katz LS, Griswold T, Lindsey RL, Lauer AC, Im MS, Williams G, Halpin JL, Gómez GA, Kucerova Z, Morrison S, Page A, Den Bakker HC, Carleton HA. 2025. "Kalamari: a representative set of genomes of public health concern." Microbiol Resour Announc 14:e00963-24. https://doi.org/10.1128/mra.00963-24