ArticleGenome biology2021
ReSeq simulates realistic Illumina high-throughput sequencing data.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis.NPJ genomic medicine · 2025Article
- Simulated High Throughput Sequencing Datasets: A Crucial Tool for Validating Bioinformatic Pathogen Detection Pipelines.Biology · 2024Article
- Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.BMC genomics · 2024Article
- Optimal adjustment sets for causal query estimation in partially observed biomolecular networks.Bioinformatics (Oxford, England) · 2023Article
- annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.GigaScience · 2022Article
- Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.Environmental microbiome · 2022Article
- From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures.Computational and structural biotechnology journal · 2022Review
- Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.Nature communications · 2021Article
- ReSeq simulates realistic Illumina high-throughput sequencing data.Genome biology · 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions at each step of a project. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools. ReSeq improves the authenticity of synthetic data by extracting and reproducing key components from real data. Major advancements are the inclusion of systematic errors, a fragment-based coverage model and sampling-matrix estimates based on two-dimensional margins. These improvements lead to more faithful performance evaluations. ReSeq is available at https://github.com/schmeing/ReSeq .
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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.