ArticleNucleic acids research2015
Reference-free detection of isolated SNPs.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 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
43 citing papers in PubMed.
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- Article
- Longitudinal and cross-sectional sampling and whole genome sequencing ofApplied and environmental microbiology · 2025Article
- A scalable distributed pipeline for reference-free variants calling.BMC genomics · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.GigaScience · 2025Article
- Space-efficient computation of k-mer dictionaries for large values of k.Algorithms for molecular biology : AMB · 2024Article
- Evaluation of Fourier transform-infrared spectroscopy (FT-IR) as a control measure for nosocomial outbreak investigations.Journal of clinical microbiology · 2023Article
- Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations.BMC ecology and evolution · 2023Article
- ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs.Molecular ecology resources · 2023Article
- Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits.PloS one · 2023Article
- Review
- Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate.Biotechnology for biofuels and bioproducts · 2022Article
- Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.Bioinformatics (Oxford, England) · 2021Article
- 2-kupl: mapping-free variant detection from DNA-seq data of matched samples.BMC bioinformatics · 2021Article
- Nebula: ultra-efficient mapping-free structural variant genotyper.Nucleic acids research · 2021Article
- Metagenome SNP calling via read-colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2021Article
- Genomic and RT-qPCR analysis of trimethoprim-sulfamethoxazole and meropenem resistance in Burkholderia pseudomallei clinical isolates.PLoS neglected tropical diseases · 2021Article
- Enabling Genomics Pipelines in Commodity Personal Computers With Flash Storage.Frontiers in genetics · 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
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, discoSnp, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, discoSnp ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, discoSnp requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism.
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.