Hecatomb: an end-to-end research platform for viral metagenomics

MJ Roach, SJ Beecroft, KA Mihindukulasuriya, L Wang… - bioRxiv, 2022 - biorxiv.org
Background Analysis of viral diversity using modern sequencing technologies offers
extraordinary opportunities for discovery. However, these analyses present a number of …

Hecatomb: an integrated software platform for viral metagenomics

MJ Roach, SJ Beecroft, KA Mihindukulasuriya… - …, 2024 - academic.oup.com
Background Modern sequencing technologies offer extraordinary opportunities for virus
discovery and virome analysis. Annotation of viral sequences from metagenomic data …

Elimination of foreign sequences in eukaryotic viral reference genomes improves the accuracy of virome analysis

J Chen, Y Sun, X Yan, Z Ren, G Wang, Y Liu, Z Zhao… - Msystems, 2022 - Am Soc Microbiol
Widespread in public databases, foreign contaminant sequences pose a substantial
obstacle in genomic analyses. Such contamination in viral genome databases is also …

Virome composition in marine fish revealed by meta-transcriptomics

JL Geoghegan, F Di Giallonardo, M Wille… - Virus …, 2021 - academic.oup.com
Revealing the determinants of virome composition is central to placing disease emergence
in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so …

VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data

P Fu, Y Wu, Z Zhang, Y Qiu, Y Wang… - Briefings in …, 2024 - academic.oup.com
Identification of viruses and further assembly of viral genomes from the next-generation-
sequencing data are essential steps in virome studies. This study presented a one-stop tool …

Maximal viral information recovery from sequence data using VirMAP

NJ Ajami, MC Wong, MC Ross, RE Lloyd… - Nature …, 2018 - nature.com
Accurate classification of the human virome is critical to a full understanding of the role
viruses play in health and disease. This implies the need for sensitive, specific, and practical …

Virus finding tools: Current solutions and limitations

GF Privitera, S Alaimo, A Ferro… - Briefings in …, 2022 - academic.oup.com
Motivation The study of the Human Virome remains challenging nowadays. Viral
metagenomics, through high-throughput sequencing data, is the best choice for virus …

ViromeScan: a new tool for metagenomic viral community profiling

S Rampelli, M Soverini, S Turroni, S Quercia, E Biagi… - Bmc Genomics, 2016 - Springer
Background Bioinformatics tools available for metagenomic sequencing analysis are
principally devoted to the identification of microorganisms populating an ecological niche …

[HTML][HTML] Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

M Asplund, KR Kjartansdóttir, S Mollerup… - Clinical Microbiology …, 2019 - Elsevier
Objectives Sample preparation for high-throughput sequencing (HTS) includes treatment
with various laboratory components, potentially carrying viral nucleic acids, the extent of …

IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning

H Yin, S Wu, J Tan, Q Guo, M Li, J Guo, Y Wang… - …, 2024 - academic.oup.com
Background The virome obtained through virus-like particle enrichment contains a mixture of
prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification …