ArticleBioinformatics (Oxford, England)2019
NGSEP3: accurate variant calling across species and sequencing protocols.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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
51 citing papers in PubMed.
- Reference-Guided Chromosome-Scale Genome Assembly With Insights on Population Genomics of the Atlantic Goliath Grouper (Ecology and evolution · 2026Article
- Breast cancer clustering integrating complete gene expression profiles and genetic ancestry.PloS one · 2026Article
- Genome-wide discovery of short sequence repeat markers useful for genetic diversity studies in Lima bean (Phaseolus lunatus L.).Scientific reports · 2025Article
- High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination.The plant genome · 2025Article
- Variation in surface protein expression leads to heterogeneous Trypanosoma cruzi populations during host cell infection.Nature communications · 2025Article
- Flavonoid pathway intermediates implicate UVR8 in functions beyond canonical UV-B signaling.Nature communications · 2025Article
- Holobiont-based genetic analysis reveals new plant and microbial markers for resistance against a root rot pathogen complex in pea.BMC plant biology · 2025Article
- Plastomic studies inform the mechanisms of edaphic adaptation in North American species in the tribe Thelypodieae (Brassicaceae).American journal of botany · 2025Article
- Genetic diversity and comparative genomics across Leishmania (Viannia) species.Communications biology · 2025Article
- Genomic characterization of Leishmania (V.) braziliensis associated with antimony therapeutic failure and variable in vitro tolerance to amphotericin B.Scientific reports · 2025Article
- GWAS-assisted and multitrait genomic prediction for improvement of seed yield and canning quality traits in a black bean breeding panel.G3 (Bethesda, Md.) · 2025Article
- Unlocking the geography of Azobé timber (Lophira alata): revealing spatial genetic structure beyond species boundaries.BMC plant biology · 2025Article
- Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.GigaScience · 2025Article
- Genetic mechanisms of axial patterning inEvolution letters · 2024Article
- Genetic diversity of Anadara tuberculosa in two localities of the Colombian Pacific Coast.Scientific reports · 2024Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches.Scientific reports · 2024Article
- Genome-wide association and genomic prediction for iron and zinc concentration and iron bioavailability in a collection of yellow dry beans.Frontiers in genetics · 2024Article
- The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes.PloS one · 2024Article
- QTL mapping for pod quality and yield traits in snap bean (Frontiers in plant science · 2024Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAccurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features.
resultsUnderstanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats. We performed extensive benchmark experiments comparing NGSEP to state-of-the-art software using real data from three sequencing protocols and four species with different distributions of repetitive elements. NGSEP consistently shows comparative accuracy and better efficiency compared to the existing solutions. We expect that this work will contribute to the continuous improvement of quality in variant calling needed for modern applications in medicine and agriculture. AVAILABILITY AND IMPLEMENTATION: NGSEP is available as open source software at http://ngsep.sf.net. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.