Arthropod Kraken2 Database v1

ContentBelow is a list of the files in this item (in addition to the README and MANIFEST files), and their description. The first three files (marked with a *) are required to run Kraken2 classifications using the database. -

• hash.k2d.gz - A hash file with all minimiser to taxon mappings (855 GB). -
• opts.k2d - A file containing all options used when building the Kraken2 database (64 B). -
• taxo.k2d - A file containing the taxonomy information used to build the database (385.9 KB). - seqid2taxid.map.gz - A file containing contig accession numbers and their corresponding taxids (810.6 MB). Note that this file is needed by Kraken2 when building the database, and as it was updated during custom building, it has been included for reference, but it is not required to use the database for classification. - genome_assembly_metadata.tsv - NCBI-generated table (tsv format, gzipped) of all reference assemblies for Arthropoda as of March 2023, which were used in the database construction. This includes columns: Assembly Accession, Assembly Name, Organism Name, Organism Infraspecific Names Breed, Organism Infraspecific Names Strain, Organism Infraspecific Names Cultival, Organism Infraspecific Names Ecotype, Organism Infraspecific Names Isolate, Organism Infraspecific Names Sex, Annotation Name, Assembly Stats Total Sequence Length, Assembly Level, Assembly Submission, and WGS project accession. How to use the database- Download the hash.k2d.gz, opts.k2d, and taxo.k2d files to the same directory (e.g. /PATH/TO/DATABASE/). - Unzip the hash.k2d.gz file. - Install or load Kraken2 to run classification on sequencing data using the database. - When running Kraken2, indicate the path to the directory (not the individual files) with the --db flag (e.g. kraken2 --db /PATH/TO/DATABASE/ ...). Note that the whole database must be loaded into memory by Kraken2 to be able to classify any sequencing reads, so ensure you have access to enough memory before running (the uncompressed hash file is around 1.1 TB). We also recommend using the Kraken2 option --memory-mapping, as it ensures the database is loaded once for all samples, instead of once for each individual sample, saving considerable time and resources. For more information on using Kraken2, see the Kraken2 wiki manual (github.com/DerrickWood/kraken2/wiki/Manual) . This database was built by Samantha López Clinton (samantha.lopezclinton@nrm) and Tom van der Valk (tom.vandervalk@nrm.se).