A complete list of all database files is available in the Hecatomb
This database consists of a collection of NEBNext and TruSeq adapters, primerB sequences, and a collection of cloning vectors that are common sources of false positives. These sequences are used in preprocessing to trim reads of non-biological contaminant sequences.
Contamination of viral metagenomes by host DNA can be a significant burden and source of false positive in viral annotation. We use a host reference genome to filter out any host reads prior to annotation. However, host genomes typically contain large amounts of virus-like and virus-derived sequence. This could lead to erroneous removal of true viral reads. We therefore must process host reference genomes to mask viral-like sequence prior to using it for preprocessing. Hecatomb comes with several processed host genomes and a tool for users to add their own genomes. See Adding your own host genome for more info.
These are the amino acid (AA) and nucleotide (NT) databases used for sequence annotation of both reads and contigs.
For each of the AA and NT databases, there is a primary viral database used for identifying reads that match a known virus,
and a secondary multi-kingdom database which is used for assigning taxonomy to either reads and contigs.
The primary AA database includes all UniProt viral protein entries clustered at 99% identity. The secondary AA database consists of the Uniclust50 database Mirdita et al. 2017 supplemented with the primary AA database. The primary NT database consists of all viral sequences in GenBank clustered at 100% identity to remove redundancy. The secondary NT database consists of a customised polymicrobial nucleotide database containing representative RefSeq genomes from Bacteria (n = 14,933), Archaea (n = 511), Fungi (n = 423), Protozoa (n = 90) and plant (n = 145) genomes.
Hecatomb utilises the NCBI taxonomy database (taxdump) with TaxonKit for converting taxon IDs into complete lineages for the output bigtable.
These are a collection of supplementary tables. Primarily, the Baltimore classifications are provided here to be merged with the bigtable annotations.