ReviewGenomics, proteomics & bioinformatics2012
Review of general algorithmic features for genome assemblers for next generation sequencers.
Review in Genomics, proteomics & bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Linear time complexity de novo long read genome assembly with GoldRush.Nature communications · 2023Article
- Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies.GigaScience · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases.Experimental biology and medicine (Maywood, N.J.) · 2021Review
- SplitStrains, a tool to identify and separate mixedMicrobial genomics · 2021Article
- Engineered yeast genomes accurately assembled from pure and mixed samples.Nature communications · 2021Article
- Empirical evaluation of methods forPeerJ. Computer science · 2021Article
- An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota.Life (Basel, Switzerland) · 2020Review
- DeepDeath: Learning to predict the underlying cause of death with Big Data.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2017Article
- The A, C, G, and T of Genome Assembly.BioMed research international · 2016Review
- GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data.Frontiers in microbiology · 2016Article
- Complete sequence of pABTJ2, a plasmid from Acinetobacter baumannii MDR-TJ, carrying many phage-like elements.Genomics, proteomics & bioinformatics · 2014Article
- Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Optimal reference sequence selection for genome assembly using minimum description length principle.EURASIP journal on bioinformatics & systems biology · 2012Article
- Review of general algorithmic features for genome assemblers for next generation sequencers.Genomics, proteomics & bioinformatics · 2012Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.
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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.