ReviewBMC genomics2014
Reference-free SNP detection: dealing with the data deluge.
Review in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
- From Metagenomes to Functional Expression of Resistance:Antibiotics (Basel, Switzerland) · 2025Article
- Plant pangenomes for crop improvement, biodiversity and evolution.Nature reviews. Genetics · 2024Review
- Pitfalls of genotyping microbial communities with rapidly growing genome collections.Cell systems · 2023Article
- Reliable genomic strategies for species classification of plant genetic resources.BMC bioinformatics · 2021Article
- 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
- Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia.PloS one · 2020Article
- Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.).Scientific reports · 2019Article
- SNPs detection by eBWT positional clustering.Algorithms for molecular biology : AMB · 2019Article
- Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data.BMC genomics · 2018Article
- Article
- Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation.PloS one · 2017Article
- GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data.BMC bioinformatics · 2016Article
- MICADo - Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method.Frontiers in genetics · 2016Article
- Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs.Bioinformatics (Oxford, England) · 2015Article
- Article
- SNP-SIG 2013: from coding to non-coding--new approaches for genomic variant interpretation.BMC genomics · 2014Article
- From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?Applications in plant sciencesArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reference-free SNP detection, that is identifying SNPs between samples directly from comparison of primary sequencing data with other primary sequencing data and not to a pre-assembled reference genome is an emergent and potentially disruptive technology that is beginning to open up new vistas in variant identification that reveals new applications in non-model organisms and metagenomics. The modern, efficient data structures these tools use enables researchers with a reference sequence to sample many more individuals with lower computing storage and processing overhead. In this article we will discuss the technologies and tools implementing reference-free SNP detection and the potential impact on studies of genetic variation in model and non-model organisms, metagenomics and personal genomics and medicine.
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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.