ArticlePloS one2013
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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.
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Who cites it
17 citing papers in PubMed.
- A scalable distributed pipeline for reference-free variants calling.BMC genomics · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs.Molecular ecology resources · 2023Article
- Review
- Review
- From the reference human genome to human pangenome: Premise, promise and challenge.Frontiers in genetics · 2022Article
- Metagenome SNP calling via read-colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2021Article
- Methods and Developments in Graphical Pangenomics.Journal of the Indian Institute of Science · 2021Review
- Enabling Genomics Pipelines in Commodity Personal Computers With Flash Storage.Frontiers in genetics · 2021Article
- Variable-order reference-free variant discovery with the Burrows-Wheeler Transform.BMC bioinformatics · 2020Article
- Pangenome Graphs.Annual review of genomics and human genetics · 2020Review
- SNPs detection by eBWT positional clustering.Algorithms for molecular biology : AMB · 2019Article
- Indel variant analysis of short-read sequencing data with Scalpel.Nature protocols · 2016Article
- SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.Nucleic acids research · 2016Article
- The challenge of small-scale repeats for indel discovery.Frontiers in bioengineering and biotechnology · 2015Review
- Reference-free detection of isolated SNPs.Nucleic acids research · 2015Article
- Reference-free SNP detection: dealing with the data deluge.BMC genomics · 2014Review
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
Abstract
Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism detection relies on having a reference genome to which reads can be aligned and variants detected. We present Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence. Bubbleparse uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively. We show that the Bubbleparse algorithm is sensitive and can detect many polymorphisms quickly and that it performs well when compared with polymorphism detection methods based on alignment to a reference in Arabidopsis thaliana. We show that the heuristic can be used to maximise the number of true polymorphisms returned, and with a proof-of-principle experiment show that Bubbleparse is very effective on data from unsequenced wild relatives of potato and enabled us to identify disease resistance linked genes quickly and easily.
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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.