Benjamin Bolduc
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CLAE: A High‐Fidelity Nanopore Sequencing Strategy for Read‐Level Viral Variant Detection and Environmental RNA Virus Discovery Open
High‐fidelity (HF) long‐read sequencing enables accurate profiling of microorganisms and pathogens at single‐molecule resolution. However, current Oxford Nanopore Technologies (ONT)—a revolutionary platform offering real‐time, portable seq…
Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages Open
Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infectio…
View article: RNA virus ecogenomics along a subarctic permafrost thaw gradient
RNA virus ecogenomics along a subarctic permafrost thaw gradient Open
Climate change thaws permafrost, which releases greenhouse gases partly from dormant microorganisms awakening and metabolizing organic matter. Though DNA viruses that infect these soil microbes have been studied, little is known on soil RN…
Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans Open
Background Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic rep…
View article: Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient
Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient Open
Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 me…
Integrating interdisciplinary data: The EMERGE Database and its broader lessons for data management best practices Open
In environmental research, cross-disciplinary analyses enable the discovery of novel insights that may not otherwise be evident. Doing these analyses efficiently requires integration of heterogeneous data into a common data structure; howe…
Virus-encoded auxiliary metabolic genes throughout the global oceans Open
Supplementary materials supporting the manuscript titled "Virus-encoded auxiliary metabolic genes throughout the global oceans".
vConTACT3 Database v220 Open
Compressed database files used by vConTACT3 to classify virus sequences. This database is version 220 and is derived from NCBI Virus RefSeq release 220, incorporating information from the Virus-Host DB (using GenBank release 257) This file…
vConTACT3 Database v220 Open
Compressed database files used by vConTACT3 to classify virus sequences. This database is version 220 and is derived from NCBI Virus RefSeq release 220, incorporating information from the Virus-Host DB (using GenBank release 257) This file…
Virus-encoded auxiliary metabolic genes throughout the global oceans Open
Supplementary materials supporting the manuscript titled "Virus-encoded auxiliary metabolic genes throughout the global oceans".
Virus-encoded auxiliary metabolic genes throughout the global oceans Open
Supplementary materials supporting the manuscript titled "Virus-encoded auxiliary metabolic genes throughout the global oceans".
MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets Open
Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal vir…
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This is the 'title': Test Zenodo upload Open
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This is the 'title': Test Zenodo upload Open
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This is the 'title': Test Zenodo upload Open
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This is the 'title': Test Zenodo upload Open
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This is the 'title': Test Zenodo upload Open
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This is the 'title': Test Zenodo upload Open
This is the 'description'
This is the 'title': Test Zenodo upload Open
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View article: Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome Open
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Ea…
KBase Narrative - Viral Analysis End-to-End Open
This pipeline processes a single metagenomic dataset (downloaded from NCBI SRA) from the Global Ocean Viromes dataset, identifies the viral sequences using VirSorter, and subsequently classifies them with vConTACT2. Along the way there are…
Additional file 3 of MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations Open
Additional file 2: Table S1. Mock communities data actual and metapop derived abundances. Table S2. Biological virome dataset population abundances. Table S3. Full codon bias usage results for all genes in Staphylococcus aureus ECT-R2.
Peer Review #2 of "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation (v0.2)" Open
Background:Viruses influence global patterns of microbial diversity and nutrient cycles.Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its …
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation Open
Background Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its…
Processing a Viral Metagenome Using iVirus v3 Open
A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user usesactual reads fromOcean Sampling Day (2014)and processes them entirely within Cy…
Preparing Data for vContact from Proteins (Cyverse) v5 Open
Preparing data for use in vContact by usingVirSorted Ocean Sampling Day (2014) contigs, using tools available inCyverse. This protocol creates a BLAST DB, BLASTs sequences, and creates a gene-to-contig mapping file. Results from this proto…
Downloading Viral Metagenome Data v1 Open
Downloading reads from the Ocean Sampling Day (2014) using fastq-dump, a tool from the SRA toolkit implemented in Cyverse.
Processing a Viral Metagenome Using iVirus v2 Open
A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user usesactual reads fromOcean Sampling Day (2014)and processes them entirely within Cy…