ReviewBriefings in bioinformatics2014
Three-stage quality control strategies for DNA re-sequencing data.
Review in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
107 citing papers in PubMed, 1 synthesis or guideline pooled it, 179 citations in OpenAlex.
- Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations.Journal of biomedical science · 2018Pooled it
- An IRAT109 NAM population: Genetic characterization and mapping utility for trait dissection in japonica rice (Oryza sativa L.).The plant genome · 2026Article
- Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions.Scientific data · 2026Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.Genome biology · 2026Article
- A Multi-assay molecular toolkit for rapid and sensitive detection of Ustilaginoidea virens the causative agent of rice false smut using PCR, qPCR, RPA, and LAMP assays.World journal of microbiology & biotechnology · 2026Article
- Genotyping-by-Sequencing Reveals Low Genetic Diversity and Pronounced Geographic Structuring in the Endangered Medicinal PlantPlants (Basel, Switzerland) · 2026Article
- Whole-genome variant of 220 Tibetan sheep from the Qinghai-Tibetan Plateau.Scientific data · 2025Article
- Bioinformatics and artificial intelligence in genomic data analysis: current advances and future directions.Molecular genetics and genomics : MGG · 2025Review
- Whole genome sequencing data of 14 indigenous Greek goats.Scientific data · 2025Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.bioRxiv : the preprint server for biology · 2025Article
- Tutorial: guidelines for quality filtering of whole-exome and whole-genome sequencing data for population-scale association analyses.Nature protocols · 2025Review
- Estimating mutation rate and characterising single nucleotide de novo mutations in pigs.Genetics, selection, evolution : GSE · 2025Article
- Transcriptional Signatures of the Right Ventricle in End-Stage Heart Failure.Pulmonary circulation · 2025Article
- Whole-genome variants resource of 298 Saanen dairy goats.Scientific data · 2025Article
- Whole-Genome Sequencing ofAnimals : an open access journal from MDPI · 2025Article
- CFTR haplotype phasing using long-read genome sequencing from ultralow input DNA.Genetics in medicine open · 2025Article
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Whole genome sequences of 70 indigenous Ethiopian cattle.Scientific data · 2024Article
- A comparative study of structural variant calling in WGS from Alzheimer's disease families.Life science alliance · 2024Article
- Whole-genome resource sequences of 57 indigenous Ethiopian goats.Scientific data · 2024Article
47 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Advances in next-generation sequencing (NGS) technologies have greatly improved our ability to detect genomic variants for biomedical research. In particular, NGS technologies have been recently applied with great success to the discovery of mutations associated with the growth of various tumours and in rare Mendelian diseases. The advance in NGS technologies has also created significant challenges in bioinformatics. One of the major challenges is quality control of the sequencing data. In this review, we discuss the proper quality control procedures and parameters for Illumina technology-based human DNA re-sequencing at three different stages of sequencing: raw data, alignment and variant calling. Monitoring quality control metrics at each of the three stages of NGS data provides unique and independent evaluations of data quality from differing perspectives. Properly conducting quality control protocols at all three stages and correctly interpreting the quality control results are crucial to ensure a successful and meaningful study.
Indexed as
Identifiers
What OpenQuestion holds
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.