Searching journal content for articles similar to Bouck et al. 8 (10): 1074.

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  1. Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
    • Ilya B. Slizovskiy,
    • Nathalie Bonin,
    • Jonathan E. Bravo,
    • Peter M. Ferm,
    • Jacob Singer,
    • Christina Boucher,
    • and Noelle R. Noyes
    Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
    ...elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining...
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  2. Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
    • Hang Dai and
    • Yongtao Guan
    Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
    ...metagenomics whole shotgun (WGS) sequencing, where the amount of unmapped reads is substantial. When applied to a WGS sequencing data set to quantify distances between metagenomics samples from various human body habitats, Nubeam recapitulates findings made by mapping-based methods and sheds light...
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  3. Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
    • Rei Kajitani,
    • Kouta Toshimoto,
    • Hideki Noguchi,
    • Atsushi Toyoda,
    • Yoshitoshi Ogura,
    • Miki Okuno,
    • Mitsuru Yabana,
    • Masayuki Harada,
    • Eiji Nagayasu,
    • Haruhiko Maruyama,
    • Yuji Kohara,
    • Asao Fujiyama,
    • Tetsuya Hayashi,
    • and Takehiko Itoh
    Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
    ..., their distributions are expected to be random, such that sufficient sequence coverage would resolve the sequence error by removing the short, thin tips. Therefore, this approach is suitable for the assembly of a huge number of short reads from a massively parallel sequencer. Despite its strong functionality, several...
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  4. Method: TransRate: reference-free quality assessment of de novo transcriptome assemblies
    • Richard Smith-Unna,
    • Chris Boursnell,
    • Rob Patro,
    • Julian M. Hibberd,
    • and Steven Kelly
    Genome Res. August 2016 26: 1134-1144; Published in Advance June 1, 2016, doi:10.1101/gr.196469.115
    ...assemblies from the NCBI Transcriptome Shotgun Archive. One hundred fifty-five assemblies from the Transcriptome Shotgun Archive were analyzed using TransRate. The quality of the reads used to generate the assemblies were also analyzed using FastQC. (A) Cumulative distribution of TransRate raw and optimized...
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  5. Method: Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
    • Dongqing Shi,
    • Jun Wu,
    • Haibao Tang,
    • Hao Yin,
    • Hongtao Wang,
    • Ran Wang,
    • Runze Wang,
    • Ming Qian,
    • Juyou Wu,
    • Kaijie Qi,
    • Zhihua Xie,
    • Zhiwen Wang,
    • Xiang Zhao,
    • and Shaoling Zhang
    Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
    ..., illustrating that the continuity of the assembly improved on phasing.Finally, previously obtained whole- shotgun (WGS) mate-pair library sequence data (2, 5, 10, 20, and 40 kb) were used to build superscaffolds (Wu et al. 2013); BAC sequence reads (250 and 500 bp) were used again to fill in gaps, and the final...
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  6. Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
    • Yehuda Brody,
    • Robert J. Kimmerling,
    • Yosef E. Maruvka,
    • David Benjamin,
    • Juniper J. Elacqua,
    • Nicholas J. Haradhvala,
    • Jaegil Kim,
    • Kent W. Mouw,
    • Kristjana Frangaj,
    • Amnon Koren,
    • Gad Getz,
    • Scott R. Manalis,
    • and Paul C. Blainey
    Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
    ...different lineages, subclones these cells (or otherwise amplifies the subject s), and shotgun sequences each subclonal population. De novo variants arising during the growth of the original population are shared between subclones and detected with high sensitivity and specificity by identifying somatic...
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  7. Method: Enhanced virome sequencing using targeted sequence capture
    • Todd N. Wylie,
    • Kristine M. Wylie,
    • Brandi N. Herter,
    • and Gregory A. Storch
    Genome Res. December 2015 25: 1910-1920; Published in Advance September 22, 2015, doi:10.1101/gr.191049.115
    ...Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed...
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  8. PERSPECTIVE: Human Whole-Genome Shotgun Sequencing
    • James L. Weber and
    • Eugene W. Myers
    Genome Res. May 1, 1997 7: 401-409; doi:10.1101/gr.7.5.401
    ...to sequence other large s via the clone-by-clone approach. A possible general strategy for sequencing other large s would be a random cDNA sequencing project, followed possibly by some radiation hybrid physical mapping of the ESTs, followed by whole- shotgunning. About a decade ago, when the Genome Project...
  9. Method: Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
    • Nicholas J. Parkinson,
    • Siarhei Maslau,
    • Ben Ferneyhough,
    • Gang Zhang,
    • Lorna Gregory,
    • David Buck,
    • Jiannis Ragoussis,
    • Chris P. Ponting,
    • and Michael D. Fischer
    Genome Res. January 2012 22: 125-133; Published in Advance November 16, 2011, doi:10.1101/gr.124016.111
    ...be demultiplexed in silico following sequencing, thereby lowering overall costs of acquiring data sets for low-complexity samples. A common starting point for template preparation for NGS platforms is random fragmentation of target DNA and addition of platform-specific adapter sequences to flanking ends. Protocols...
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  10. METHODS: ARACHNE: A Whole-Genome Shotgun Assembler
    • Serafim Batzoglou,
    • David B. Jaffe,
    • Ken Stanley,
    • Jonathan Butler,
    • Sante Gnerre,
    • Evan Mauceli,
    • Bonnie Berger,
    • Jill P. Mesirov,
    • and Eric S. Lander
    Genome Res. January 1, 2002 12: 177-189; doi:10.1101/gr.208902
    ...computer system, called ARACHNE , for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before...
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