Searching journal content for articles similar to Joseph et al. 32 (3): 558.

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  1. Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
    • Marcus W. Fedarko,
    • Mikhail Kolmogorov,
    • and Pavel A. Pevzner
    Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
    ...for estimating the FDRs of identified mutations that can bypass the need for a simulation model and should be applicable to arbitrary long and accurate sequencing data.Phasing rare mutations in HiFi metagenomic dataGiven a set of identified mutations in a meta, the next step in assembling strains of a microbe...
  2. Method: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    • Zhoutao Chen,
    • Long Pham,
    • Tsai-Chin Wu,
    • Guoya Mo,
    • Yu Xia,
    • Peter L. Chang,
    • Devin Porter,
    • Tan Phan,
    • Huu Che,
    • Hao Tran,
    • Vikas Bansal,
    • Justin Shaffer,
    • Pedro Belda-Ferre,
    • Greg Humphrey,
    • Rob Knight,
    • Pavel Pevzner,
    • Son Pham,
    • Yong Wang,
    • and Ming Lei
    Genome Res. June 2020 30: 898-909; Published in Advance June 15, 2020, doi:10.1101/gr.260380.119
    ...are not individual microbial isolates. These kinds of metagenomic samples bring new challenges for sequencing technology. It demands long sequencing read length, low-input library construction, and optimized assemblers with minimized chimeric rate across different species. We are exploring TELL-seq for metagenomic...
  3. Review: Accurate and complete genomes from metagenomes
    • Lin-Xing Chen,
    • Karthik Anantharaman,
    • Alon Shaiber,
    • A. Murat Eren,
    • and Jillian F. Banfield
    Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
    ...binned together in this MAG across multiple samples from the same person through metagenomic read recruitment. Organizing contigs based on their sequence composition and differential coverage patterns across three samples revealed two distinct clusters (Fig. 3), the smaller one of which contained 11...
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  4. Perspective: A vision for ubiquitous sequencing
    • Yaniv Erlich
    Genome Res. October 2015 25: 1411-1416; doi:10.1101/gr.191692.115
    ...of the person’s identity. Another application for rapid DNA-based sequencing is human identification at security check-points such as airports. While other biometric signatures such as fingerprints and physiometric properties are accurate and easy to obtain, DNA has the advantage of positive identification...
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  5. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...for methylation.Initially, the adoption of long-read sequencing technologies suffered from both high error rates, at times up to 30%, and high costs, which have so far been significantly reduced over time (Fig. 1B). Currently, PacBio HiFi and ONT generate highly accurate long reads, exceeding 99% accuracy...
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