ArticleBriefings in bioinformatics2021
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 28 citations in OpenAlex.
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- The N6-methyladenosine writer METTL3 promotes breast cancer progression through YTHDF2-dependent posttranscriptional silencing of GSDMD.Apoptosis : an international journal on programmed cell death · 2025Article
- BonoboFlow: viral genome assembly and haplotype reconstruction from nanopore reads.Bioinformatics advances · 2025Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.Microbiome · 2024Article
- Human cytomegalovirus harnesses host L1 retrotransposon for efficient replication.Nature communications · 2024Article
- Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples.Microbial genomics · 2023Article
- Assembling Quality Genomes of Flax Fungal Pathogens from Oxford Nanopore Technologies Data.Journal of fungi (Basel, Switzerland) · 2023Article
- Article
- High-throughput engineering of cytoplasmic- and nuclear-replicating large dsDNA viruses by CRISPR/Cas9.The Journal of general virology · 2022Article
- A general approach to identify low-frequency variants within influenza samples collected during routine surveillance.Microbial genomics · 2022Article
- Is the reductionist paradox an Achilles Heel of drug discovery?Journal of computer-aided molecular design · 2022Article
- VirStrain: a strain identification tool for RNA viruses.Genome biology · 2022Article
- Promising Role of Emodin as Therapeutics to Against Viral Infections.Frontiers in pharmacology · 2022Review
- Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples.Virus evolution · 2022Article
- Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics.Plants (Basel, Switzerland) · 2021Review
- Herpes simplex virus 2 (HSV-2) evolves faster in cell culture than HSV-1 by generating greater genetic diversity.PLoS pathogens · 2021Article
- Haploflow: strain-resolved de novo assembly of viral genomes.Genome biology · 2021Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencing of clinical specimens requires the accurate assembly of individual strains or sequence variants and suitable variant calling methods. However, the performance of most methods has not been assessed for populations composed of low divergent viral strains with large genomes, such as HCMV. In an extensive benchmarking study, we evaluated 15 assemblers and 6 variant callers on 10 lab-generated benchmark data sets created with two different library preparation protocols, to identify best practices and challenges for analyzing such data. Most assemblers, especially metaSPAdes and IVA, performed well across a range of metrics in recovering abundant strains. However, only one, Savage, recovered low abundant strains and in a highly fragmented manner. Two variant callers, LoFreq and VarScan2, excelled across all strain abundances. Both shared a large fraction of false positive variant calls, which were strongly enriched in T to G changes in a 'G.G' context. The magnitude of this context-dependent systematic error is linked to the experimental protocol. We provide all benchmarking data, results and the entire benchmarking workflow named QuasiModo, Quasispecies Metric determination on omics, under the GNU General Public License v3.0 (https://github.com/hzi-bifo/Quasimodo), to enable full reproducibility and further benchmarking on these and other data.
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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.