ArticlePloS one2011
Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 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.
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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 Promising Strain for Wheat Growth Promotion and Antifungal Activity Against Fungal Phytopathogens:Microorganisms · 2026Article
- An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.BMC genomics · 2024Article
- Archaeal Communities: The Microbial Phylogenomic Frontier.Frontiers in genetics · 2021Review
- Perfluorobutane sulfonate exposure disrupted human placental cytotrophoblast cell proliferation and invasion involving in dysregulating preeclampsia related genes.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective.Evolutionary bioinformatics online · 2018Article
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- Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing.BMC genomics · 2015Article
- Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.PloS one · 2015Article
- Correcting for sequencing error in maximum likelihood phylogeny inference.G3 (Bethesda, Md.) · 2014Article
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- Impact of analytic provenance in genome analysis.BMC genomics · 2014Article
- Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.Nucleic acids research · 2013Article
- Sequence assembly demystified.Nature reviews. Genetics · 2013Review
- Next-generation sequence assembly: four stages of data processing and computational challenges.PLoS computational biology · 2013Review
- Article
- TIGER: tiled iterative genome assembler.BMC bioinformatics · 2012Article
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent developments in high-throughput sequencing technology have made low-cost sequencing an attractive approach for many genome analysis tasks. Increasing read lengths, improving quality and the production of increasingly larger numbers of usable sequences per instrument-run continue to make whole-genome assembly an appealing target application. In this paper we evaluate the feasibility of de novo genome assembly from short reads (≤100 nucleotides) through a detailed study involving genomic sequences of various lengths and origin, in conjunction with several of the currently popular assembly programs. Our extensive analysis demonstrates that, in addition to sequencing coverage, attributes such as the architecture of the target genome, the identity of the used assembly program, the average read length and the observed sequencing error rates are powerful variables that affect the best achievable assembly of the target sequence in terms of size and correctness.
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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.