A database of completed assemblies for metagenomics-related tasks
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.
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_KEYenvironmental variableEMAILenvironmental 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 protected]
using your own email address instead of [email protected].
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
How to format and query databases
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.
Please see CONTRIBUTING.md
Please refer to the ASM 2018 poster under docs.