ArticleGigaScience2020
A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- DNA Virus Detection in Olfactory Neuroblastomas Using Targeted Enrichment NGS.Neuropathology : official journal of the Japanese Society of Neuropathology · 2026Article
- EBV genome analysis in multiple sclerosis shows extensive viral diversity and links to autoimmunity.NAR molecular medicine · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- ViromeXplore: integrative workflows for complete and reproducible virome characterization.Briefings in bioinformatics · 2025Article
- Reactivation of a Transplant Recipient's Inherited Human Herpesvirus 6 and Implications to the Graft.The Journal of infectious diseases · 2025Article
- Multiple DNA Viruses and HPV Integration in Inverted Papilloma and Associated Sinonasal Carcinoma.The Laryngoscope · 2025Article
- A lossless reference-free sequence compression algorithm leveraging grammatical, statistical, and substitution rules.Briefings in functional genomics · 2025Article
- Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.Nucleic acids research · 2024Article
- Presence of herpesviruses, parvoviruses, and polyomaviruses in sinonasal lymphoma.European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery · 2024Article
- Article
- ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance.NAR genomics and bioinformatics · 2024Article
- Article
- Unmasking the tissue-resident eukaryotic DNA virome in humans.Nucleic acids research · 2023Article
- Herpesviruses, polyomaviruses, parvoviruses, papillomaviruses, and anelloviruses in vestibular schwannoma.Journal of neurovirology · 2023Article
- AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.GigaScience · 2022Article
- Review
- Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement.BMC genomics · 2022Article
- Article
- Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.PloS one · 2022Article
- The Human Bone Marrow Is Host to the DNAs of Several Viruses.Frontiers in cellular and infection microbiology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAdvances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data.
findingsTRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs.
conclusionsTRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.