ArticleGenome biology2017
A comparative evaluation of genome assembly reconciliation tools.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed.
- The draft genome sequence of the ascomycete fungusMicrobiology resource announcements · 2026Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness.Scientific reports · 2025Article
- Autocycler: long-read consensus assembly for bacterial genomes.Bioinformatics (Oxford, England) · 2025Article
- A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes.Nucleic acids research · 2024Article
- Investigating the Quantification Capabilities of a Nanopore-Based Sequencing Platform for Food Safety Application via External Standards of Lambda DNA and Lambda Spiked Beef.Foods (Basel, Switzerland) · 2024Article
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.Nature communications · 2024Article
- Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.Genome research · 2024Article
- First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies.G3 (Bethesda, Md.) · 2024Article
- Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii.BMC genomics · 2023Article
- Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae.G3 (Bethesda, Md.) · 2023Article
- Substrate Specificity of Biofilms Proximate to Historic Shipwrecks.Microorganisms · 2023Article
- A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera).BMC genomics · 2023Article
- Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates.BMC microbiology · 2023Article
- Long-read genome assemblies for the study of chromosome expansion:bioRxiv : the preprint server for biology · 2023Article
- Insight into the Organization of the B10v3 Cucumber Genome by Integration of Biological and Bioinformatic Data.International journal of molecular sciences · 2023Article
- Improvements to the Gulf pipefishGigaByte (Hong Kong, China) · 2023Article
- Accelerating Minimap2 for Accurate Long Read Alignment on GPUs.Journal of biotechnology and biomedicine · 2023Article
- Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.Genome biology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation.
resultsSeveral assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input.
conclusionsNone of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assemblies already have high quality. In terms of correctness, the quality of the results depends on the specific tool, as well as on the quality and the ranking of the input assemblies. In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.
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.