ReviewPLoS computational biology2013
Next-generation sequence assembly: four stages of data processing and computational challenges.
Review in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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.
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.
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Who cites it
41 citing papers in PubMed.
- plsMD: a plasmid reconstruction tool from short-read assemblies.BMC bioinformatics · 2026Article
- Bioinformatics and artificial intelligence in genomic data analysis: current advances and future directions.Molecular genetics and genomics : MGG · 2025Review
- MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads.BMC bioinformatics · 2024Article
- Approaches to increase the validity of gene family identification using manual homology search tools.Genetica · 2023Review
- Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?Microorganisms · 2023Review
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades.Journal of medical virology · 2021Article
- Article
- Mutation-selection balance and compensatory mechanisms in tumour evolution.Nature reviews. Genetics · 2021Review
- Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists.Scientific reports · 2020Article
- A Novel Field-Deployable Method for Sequencing and Analyses of Henipavirus Genomes From Complex Samples on the MinION Platform.The Journal of infectious diseases · 2020Article
- On Variant Discovery in Genomes of Fungal Plant Pathogens.Frontiers in microbiology · 2020Article
- Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook.Malaria journal · 2019Article
- Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Relating Phage Genomes toInternational journal of molecular sciences · 2018Review
- Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease.Journal of visualized experiments : JoVE · 2018Article
- Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.PloS one · 2018Article
- Coordinate systems for supergenomes.Algorithms for molecular biology : AMB · 2018Article
- Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).BMC biology · 2017Article
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
No grant is acknowledged in the PubMed record.
Abstract
Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we address the basic framework of next-generation genome sequence assemblers, which comprises four basic stages: preprocessing filtering, a graph construction process, a graph simplification process, and postprocessing filtering. Here we discuss them as a framework of four stages for data analysis and processing and survey variety of techniques, algorithms, and software tools used during each stage. We also discuss the challenges that face current assemblers in the next-generation environment to determine the current state-of-the-art. We recommend a layered architecture approach for constructing a general assembler that can handle the sequences generated by different sequencing platforms.
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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.