Výsledky vyhledávání - "Phillippy, Adam M"

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies Autor Rhie, Arang, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M.

“…Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a…”
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One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly Autor Koren, Sergey, Phillippy, Adam M

“…•We describe three long-read sequencing technologies and their characteristics.•We describe available algorithms for long-read assembly and their use.•Most…”
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Long-read mapping to repetitive reference sequences using Winnowmap2 Autor Jain, Chirag, Rhie, Arang, Hansen, Nancy F., Koren, Sergey, Phillippy, Adam M.

“…Approximately 5–10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat…”
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Interactive metagenomic visualization in a Web browser Autor Ondov, Brian D, Bergman, Nicholas H, Phillippy, Adam M

“…Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in…”
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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Autor Jain, Chirag, Rodriguez-R, Luis M., Phillippy, Adam M., Konstantinidis, Konstantinos T., Aluru, Srinivas

“…A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead…”
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The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes Autor Treangen, Todd J, Ondov, Brian D, Koren, Sergey, Phillippy, Adam M

“…Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to…”
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MUMmer4: A fast and versatile genome alignment system Autor Marçais, Guillaume, Delcher, Arthur L., Phillippy, Adam M., Coston, Rachel, Salzberg, Steven L., Zimin, Aleksey

“…The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major…”
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Weighted minimizer sampling improves long read mapping Autor Jain, Chirag, Rhie, Arang, Zhang, Haowen, Chu, Claudia, Walenz, Brian P, Koren, Sergey, Phillippy, Adam M

“…Abstract Motivation In this era of exponential data growth, minimizer sampling has become a standard algorithmic technique for rapid genome sequence…”
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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads Autor Nurk, Sergey, Walenz, Brian P, Rhie, Arang, Vollger, Mitchell R, Logsdon, Glennis A, Grothe, Robert, Miga, Karen H, Eichler, Evan E, Phillippy, Adam M, Koren, Sergey

“…Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have…”
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Integrating Hi-C links with assembly graphs for chromosome-scale assembly Autor Ghurye, Jay, Rhie, Arang, Walenz, Brian P., Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M., Koren, Sergey

“…Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In…”
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Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps Autor Dilthey, Alexander T., Jain, Chirag, Koren, Sergey, Phillippy, Adam M.

“…Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance…”
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A fast adaptive algorithm for computing whole-genome homology maps Autor Jain, Chirag, Koren, Sergey, Dilthey, Alexander, Phillippy, Adam M, Aluru, Srinivas

“…Abstract Motivation Whole-genome alignment is an important problem in genomics for comparing different species, mapping draft assemblies to reference genomes…”
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Mash Screen: high-throughput sequence containment estimation for genome discovery Autor Ondov, Brian D., Starrett, Gabriel J., Sappington, Anna, Kostic, Aleksandra, Koren, Sergey, Buck, Christopher B., Phillippy, Adam M.

“…The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate…”
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RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification Autor Nasko, Daniel J., Koren, Sergey, Phillippy, Adam M., Treangen, Todd J.

“…In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k -mer-based lowest…”
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Hybrid error correction and de novo assembly of single-molecule sequencing reads Autor Koren, Sergey, Schatz, Michael C, Walenz, Brian P, Martin, Jeffrey, Howard, Jason T, Ganapathy, Ganeshkumar, Wang, Zhong, Rasko, David A, McCombie, W Richard, Jarvis, Erich D, Phillippy, Adam M

“…Single-molecule sequencing technologies can produce multikilobase-long reads, which are more useful than short reads for assembling genomes and transcriptomes,…”
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ModDotPlot—rapid and interactive visualization of tandem repeats Autor Sweeten, Alexander P, Schatz, Michael C, Phillippy, Adam M

“…Abstract Motivation A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches…”
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The structure, function and evolution of a complete human chromosome 8 Autor Logsdon, Glennis A., Vollger, Mitchell R., Hsieh, PingHsun, Mao, Yafei, Liskovykh, Mikhail A., Koren, Sergey, Nurk, Sergey, Mercuri, Ludovica, Dishuck, Philip C., Rhie, Arang, de Lima, Leonardo G., Dvorkina, Tatiana, Porubsky, David, Harvey, William T., Mikheenko, Alla, Bzikadze, Andrey V., Kremitzki, Milinn, Graves-Lindsay, Tina A., Jain, Chirag, Hoekzema, Kendra, Murali, Shwetha C., Munson, Katherine M., Baker, Carl, Sorensen, Melanie, Lewis, Alexandra M., Surti, Urvashi, Gerton, Jennifer L., Larionov, Vladimir, Ventura, Mario, Miga, Karen H., Phillippy, Adam M., Eichler, Evan E.

“…The complete assembly of each human chromosome is essential for understanding human biology and evolution 1 , 2 . Here we use complementary long-read…”
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Epigenetic patterns in a complete human genome Autor Gershman, Ariel, Sauria, Michael E G, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H, Timp, Winston

“…The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous…”
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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements Autor Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick G S, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian F A, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H, O'Neill, Rachel J

“…Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive…”
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HLALA—HLA typing from linearly projected graph alignments Autor Dilthey, Alexander T, Mentzer, Alexander J, Carapito, Raphael, Cutland, Clare, Cereb, Nezih, Madhi, Shabir A, Rhie, Arang, Koren, Sergey, Bahram, Seiamak, McVean, Gil, Phillippy, Adam M

“…Abstract Summary HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments…”
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