ArticlePloS one2011
Error and error mitigation in low-coverage genome assemblies.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- COATi: Statistical Pairwise Alignment of Protein-Coding Sequences.Molecular biology and evolution · 2024Article
- An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.BMC genomics · 2024Article
- Revised eutherian gene collections.BMC genomic data · 2022Article
- Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow EndemicFrontiers in plant science · 2022Article
- CoelacanthJournal of virology · 2021Article
- Comparative genomic analysis of eutherian fibroblast growth factor genes.BMC genomics · 2020Article
- Comparative analysis of corrected tiger genome provides clues to its neuronal evolution.Scientific reports · 2019Article
- Referee: Reference Assembly Quality Scores.Genome biology and evolution · 2019Article
- Article
- Article
- Extensive error in the number of genes inferred from draft genome assemblies.PLoS computational biology · 2014Article
- The role of replicates for error mitigation in next-generation sequencing.Nature reviews. Genetics · 2014Review
- Article
- Article
- The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments.Trends in ecology & evolution · 2013Article
- Next-generation sequence assembly: four stages of data processing and computational challenges.PLoS computational biology · 2013Review
- Article
- Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown.Proceedings. Biological sciences · 2012Article
- A modular assembly cloning technique (aided by the BIOF software tool) for seamless and error-free assembly of long DNA fragments.BMC research notes · 2012Article
- Controversies in modern evolutionary biology: the imperative for error detection and quality control.BMC genomics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The recent release of twenty-two new genome sequences has dramatically increased the data available for mammalian comparative genomics, but twenty of these new sequences are currently limited to ∼2× coverage. Here we examine the extent of sequencing error in these 2× assemblies, and its potential impact in downstream analyses. By comparing 2× assemblies with high-quality sequences from the ENCODE regions, we estimate the rate of sequencing error to be 1-4 errors per kilobase. While this error rate is fairly modest, sequencing error can still have surprising effects. For example, an apparent lineage-specific insertion in a coding region is more likely to reflect sequencing error than a true biological event, and the length distribution of coding indels is strongly distorted by error. We find that most errors are contributed by a small fraction of bases with low quality scores, in particular, by the ends of reads in regions of single-read coverage in the assembly. We explore several approaches for automatic sequencing error mitigation (SEM), making use of the localized nature of sequencing error, the fact that it is well predicted by quality scores, and information about errors that comes from comparisons across species. Our automatic methods for error mitigation cannot replace the need for additional sequencing, but they do allow substantial fractions of errors to be masked or eliminated at the cost of modest amounts of over-correction, and they can reduce the impact of error in downstream phylogenomic analyses. Our error-mitigated alignments are available for download.
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.