A database of completed assemblies for metagenomics-related tasks
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.
For usage, run perl bin/downloadKalamari.pl --help
SRC=Kalamari
perl bin/downloadKalamari.pl -o $SRC src/chromosomes.tsv
SRC=Kalamari
perl bin/downloadKalamari.pl -o $SRC src/chromosomes.tsv src/plasmids.tsv
The taxonomy files nodes.dmp and names.dmp are under src/taxonomy-VER
where VER is the version of Kalamari.
After you create your Kalamari database(s), here is how to use them
Please refer to the ASM 2018 poster under docs