The Reference Libraries

---

maxThree for Taxonomy and Tool 4

The maxThree reference library contains genome assemblies of lactic acid bacteria. Three strains of every species within the following Genera are included:

• all Genera from the newly named Lactobacillaceae* family
• the Genera Enterococcus,
• the Genera Carnobacterium, and
• the Genera Lactococcus.

* see below for a list of the Genera with family Lactobacillaceae.

The genomes are downloaded from the RefSeq database. The strains with the highest specifications are included. For some species, data for fewer than three strains is available.

File names are Genus_species_strain, and are cleaned to remove any spaces, colons, backslashes and additional information.

For the Core Taxonomy module, the files are saved as .fna in a folder named fna_YYYY-MM-DD. A separate folder containing lists of all the downloaded strains is also generated, fna_ref_lists_YYYY-MM-DD/.

For Tool 4, the files are saved as .fasta in a folder named tool4_fasta_YYYY-MM-DD.

---

maxOne for Phylogeny

The Core uses the maxOne reference library to generate a phylogenetic tree. Like maxThree, the maxOne reference library also contains genome assemblies of lactic acid bacteria.

One strains of every species within the newly named Lactobacillaceae* family are included.

* see below for a list of the Genera with family Lactobacillaceae.

This library is made using a similar script to maxThree, however in this case a single genome for each species is included. File names are Genus_species_strain, and are cleaned to remove any spaces, colons, backslashes and additional information. They are saved as .fasta in a folder named fasta_YYYY-MM-DD.

---

kraken2

kraken2 databases are required by three different processes in the Core Tool:

• kraken2_QC determines if contamination is present in the raw reads,
• kraken2 is used to determine the Genus of each query strain and
• kraken2_miniKraken provides taxonomy information if the isolate is of an unexpected Genus.

---