Cenote-Taker 2 democratizes virus discovery and sequence annotation

Abstract

Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as ‘hypothetical protein’ or the equivalent. Cenote-Taker 2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker 2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker 2 to facilitate virus discovery, annotation, and expansion of the known virome.

A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

“…Cenote-Taker 2 ( 33 ) was used to check contigs for two common end features of complete viral genomes: direct terminal repeats (DTRs) (suggesting a circular or long terminal repeat–bounded viral genome) or inverted terminal repeats (ITRs). Sequences with DTRs were arbitrarily assumed to represent circular DNA genomes.…”

“…The current study sought to overcome the traditional challenges of sparse viral databases and poor detection of highly divergent viral sequences by using Cenote-Taker 2, a new virus discovery and annotation tool ( 33 ). The pipeline was applied to sequencing data from nearly 6,000 human metagenome samples.…”

A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

“…To understand the functional potential of the viruses in the DEVoC, we predicted viral genes and annotated them using Cenote-Taker 2 ( 49 ). The 190,029 DEVoC genes ranged in size from 0.06 to 18.2 kb (median, 0.34 kb; interquartile range [IQR], 0.19 to 0.62 kb), and 91.3% were complete.…”

“…Thus, viral taxonomic analysis is mostly performed on scaffold level or on artificial taxonomic levels generated by gene-sharing tools, e.g., vConTACT2 ( 47 ) or GRAViTy ( 48 ). Finally, the lack of host information and functional annotation of proteins complicates the characterization of the phages and their interactions with bacteria in the gut ( 23 , 49 ). The technical difficulties of identifying and characterizing viruses are numerous.…”

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)

“…A total of 59,515 viral contigs were predicted using the Cenote-Taker 2 pipeline ( 17 ). An NMDS plot, with a stress value of 0.09, was constructed based on the Bray-Curtis dissimilarity of the relative abundances of the viral contigs in each sample ( Fig.…”