Hecatomb: An End-to-End Research Platform for Viral Metagenomics

Background Analysis of viral diversity using modern sequencing technologies offers extraordinary opportunities for discovery. However, these analyses present a number of bioinformatic challenges due to viral genetic diversity and virome complexity. Due to the lack of conserved marker sequences, metagenomic detection of viral sequences requires a non-targeted, random (shotgun) approach. Annotation and enumeration of viral sequences relies on rigorous quality control and effective search strategies against appropriate reference databases. Virome analysis also benefits from the analysis of both individual metagenomic sequences as well as assembled contigs. Combined, virome analysis results in large amounts of data requiring sophisticated visualization and statistical tools. Results Here we introduce Hecatomb, a bioinformatics platform enabling both read and contig based analysis. Hecatomb integrates query information from both amino acid and nucleotide reference sequence databases. Hecatomb integrates data collected throughout the workflow enabling analyst driven virome analysis and discovery. Hecatomb is available on GitHub at . Conclusions Hecatomb provides a single, modular software solution to the complex tasks required of many virome analysis. We demonstrate the value of the approach by applying Hecatomb to both a host-associated (enteric) and an environmental (marine) virome data set. Hecatomb provided data to determine true- or false-positive viral sequences in both data sets and revealed complex virome structure at distinct marine reef sites. ### Competing Interest Statement The authors have declared no competing interest. * AIDS : acquired immunodeficiency syndrome SIV : simian immunodeficiency virus HPC : high-performance computing NCBI : National Center for Biotechnology Information RPKM : reads per kilobase million FPKM : fragments per kilobase million SPM : sequences per million LCA : lowest common ancestor ICTV : International Committee on Taxonomy of Viruses PERMANOVA : permutational analysis of variance PCoA : principal coordinate analysis ANOVA : analysis of variance SIMPER : similarity percentag