ArticleScientific reports2013
Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- FGenes · 2025Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes.BMC bioinformatics · 2021Article
- Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution.Neotropical entomology · 2021Review
- One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.PLoS computational biology · 2021Article
- Read trimming has minimal effect on bacterial SNP-calling accuracy.Microbial genomics · 2020Article
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.GigaScience · 2020Article
- Article
- Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution.BMC genomics · 2018Article
- Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions.Bioinformatics (Oxford, England) · 2017Article
- Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis.Genome biology and evolution · 2017Article
- Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi.Nature communications · 2017Article
- Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Article
- Cascade: an RNA-seq visualization tool for cancer genomics.BMC genomics · 2016Article
- Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error.BMC research notes · 2015Article
- An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.BMC bioinformatics · 2015Article
- Characterizing Benzo[a]pyrene-induced lacZ mutation spectrum in transgenic mice using next-generation sequencing.BMC genomics · 2015Article
- Article
- Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach.BMC genomics · 2014Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the overall accuracies of an input read dataset, alignment and SNP-calling method providing an isolate in that dataset has a corresponding, or closely related reference sequence available. In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate. We benchmark this method against other SNP callers using our FDR method with three fungal genomes, finding that it was able achieve a high level of accuracy. These tools are available at http://cfdr.sourceforge.net/.
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.