Searching journal content for articles similar to Hsi-Yang Fritz et al. 21 (5): 734.

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Method: A privacy-preserving solution for compressed storage and selective retrieval of genomic data
- Zhicong Huang,
- Erman Ayday,
- Huang Lin,
- Raeka S. Aiyar,
- Adam Molyneaux,
- Zhenyu Xu,
- Jacques Fellay,
- Lars M. Steinmetz,
- and Jean-Pierre Hubaux
Genome Res. December 2016 26: 1687-1696; Published in Advance October 27, 2016, doi:10.1101/gr.206870.116
...compression to the data blocks. Various advanced compression algorithms have been proposed for high-throughput DNA sequence data (Quip [Jones et al. 2012], Samcomp [Bonfield and Mahoney 2013], HUGO [Li et al. 2014], etc.). Among larger data sets (e.g., The 1000 Genomes Project Consortium...
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Resource: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- Aaron McKenna,
- Matthew Hanna,
- Eric Banks,
- Andrey Sivachenko,
- Kristian Cibulskis,
- Andrew Kernytsky,
- Kiran Garimella,
- David Altshuler,
- Stacey Gabriel,
- Mark Daly,
- and Mark A. DePristo
Genome Res. September 2010 20: 1297-1303; Published in Advance July 19, 2010, doi:10.1101/gr.107524.110
...designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific...
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Method: Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
- Dirk D. Dolle,
- Zhicheng Liu,
- Matthew Cotten,
- Jared T. Simpson,
- Zamin Iqbal,
- Richard Durbin,
- Shane A. McCarthy,
- and Thomas M. Keane
Genome Res. February 2017 27: 300-309; Published in Advance December 16, 2016, doi:10.1101/gr.211748.116
...evidence for 0.13% of reads coming from nonhuman DNA (Tae et al. 2014). To expand this to the full set of samples, we downloaded 257,943 viral sequences from the CoreNucleotide division ofGenBank andused theKraken classifier (Wood and Salzberg 2014) to define a set of 102.6M virus-specific 31-mers (see...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can...
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Method: Effective sequence similarity detection with strobemers
- Kristoffer Sahlin
Genome Res. November 2021 31: 2080-2094; Published in Advance October 19, 2021, doi:10.1101/gr.275648.121
...of the strobemers are discussed in detail in the Methods section. The name strobemers is inspired by strobe sequencing technology (an early Pacific Biosciences sequencing protocol), which would produce multiple subreads from a single contiguous fragment of DNA in which the subreads were separated by “dark...
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Resource: Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
...nearly half a petabyte of temporary storage and 1.05 million CPU hours on a new cluster (Catalyst) designed for data intensive computing (see Methods). Table 2 shows a count of distinct human labeled 20-mers added from each source of human genomic DNA: the reference assembly (LMAT-Ref), GenBank (LMAT...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
...assembly using long-read data from third-generation sequencing is a viable strategy for overcoming reference bias and assembling through highly repetitive loci (Rhoads and Au 2015; Jain et al. 2018). However, the high-molecular-weight gDNA input requirement relative to second-generation sequencing (∼5000...
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Perspective: Biological data sciences in genome research
- Michael C. Schatz
Genome Res. October 2015 25: 1417-1422; doi:10.1101/gr.191684.115
.... Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res 21: 734–740. TheHumanMicrobiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207–214. Illumina. 2015.HiSeq X series of sequencing systems. Vol...
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Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
- Valerie A. Schneider,
- Tina Graves-Lindsay,
- Kerstin Howe,
- Nathan Bouk,
- Hsiu-Chuan Chen,
- Paul A. Kitts,
- Terence D. Murphy,
- Kim D. Pruitt,
- Françoise Thibaud-Nissen,
- Derek Albracht,
- Robert S. Fulton,
- Milinn Kremitzki,
- Vincent Magrini,
- Chris Markovic,
- Sean McGrath,
- Karyn Meltz Steinberg,
- Kate Auger,
- William Chow,
- Joanna Collins,
- Glenn Harden,
- Timothy Hubbard,
- Sarah Pelan,
- Jared T. Simpson,
- Glen Threadgold,
- James Torrance,
- Jonathan M. Wood,
- Laura Clarke,
- Sergey Koren,
- Matthew Boitano,
- Paul Peluso,
- Heng Li,
- Chen-Shan Chin,
- Adam M. Phillippy,
- Richard Durbin,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
...-satellite repeats in a manner proportional to that observed in the initial read database, but the long-range ordering of repeats is inferred. In contrast to the remainder of the chromosome sequence, in which each underlying clone component represents the actual haplotype of its source DNA, the modeled sequence...
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