ArticleBriefings in bioinformatics2021
ngsComposer: an automated pipeline for empirically based NGS data quality filtering.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Microbial-type terpene synthases enable enhanced insect and fungal resistance in engineered plants.Biodesign research · 2026Article
- Transformative Applications and Innovations in Next-Generation Sequencing Data Analysis.Journal of applied genetics · 2026Review
- Genome-wide association study identifies quantitative trait loci associated with resistance to Verticillium dahliae race 3 in tomato.The plant genome · 2025Article
- Article
- Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.Journal of assisted reproduction and genetics · 2025Article
- Genome-wide associations of sweetpotato metabolites enhance genomic prediction and identify genes in metabolic and regulatory pathways.Scientific reports · 2025Article
- Genome-Wide Association Study of Sweet Potato Storage Root Traits Using GWASpoly, a Gene Dosage-Sensitive Model.International journal of molecular sciences · 2024Article
- Establishing African genomics and bioinformatics programs through annual regional workshops.Nature genetics · 2024Review
- Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato.Horticulture research · 2024Article
- Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes.Briefings in bioinformatics · 2023Article
- A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist").G3 (Bethesda, Md.) · 2023Article
- Development of Genomic Resources in MexicanGenes · 2022Article
- Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Frontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) enables massively parallel acquisition of large-scale omics data; however, objective data quality filtering parameters are lacking. Although a useful metric, evidence reveals that platform-generated Phred values overestimate per-base quality scores. We have developed novel and empirically based algorithms that streamline NGS data quality filtering. The pipeline leverages known sequence motifs to enable empirical estimation of error rates, detection of erroneous base calls and removal of contaminating adapter sequence. The performance of motif-based error detection and quality filtering were further validated with read compression rates as an unbiased metric. Elevated error rates at read ends, where known motifs lie, tracked with propagation of erroneous base calls. Barcode swapping, an inherent problem with pooled libraries, was also effectively mitigated. The ngsComposer pipeline is suitable for various NGS protocols and platforms due to the universal concepts on which the algorithms are based.
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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.