Search Results - "Schatz, Michael C."

Assemblytics: a web analytics tool for the detection of variants from an assembly by Nattestad, Maria, Schatz, Michael C

“…Assemblytics is a web app for detecting and analyzing variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor…”
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GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes by Ranallo-Benavidez, T. Rhyker, Jaron, Kamil S., Schatz, Michael C.

“…An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed…”
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Piercing the dark matter: bioinformatics of long-range sequencing and mapping by Sedlazeck, Fritz J., Lee, Hayan, Darby, Charlotte A., Schatz, Michael C.

“…Several new genomics technologies have become available that offer long-read sequencing or long-range mapping with higher throughput and higher resolution…”
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Accurate detection of complex structural variations using single-molecule sequencing by Sedlazeck, Fritz J., Rescheneder, Philipp, Smolka, Moritz, Fang, Han, Nattestad, Maria, von Haeseler, Arndt, Schatz, Michael C.

“…Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule…”
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RaGOO: fast and accurate reference-guided scaffolding of draft genomes by Alonge, Michael, Soyk, Sebastian, Ramakrishnan, Srividya, Wang, Xingang, Goodwin, Sara, Sedlazeck, Fritz J, Lippman, Zachary B, Schatz, Michael C

“…We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve…”
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Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing by Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B, Schatz, Michael C, Soyk, Sebastian

“…Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for…”
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GenomeScope: fast reference-free genome profiling from short reads by Vurture, Gregory W, Sedlazeck, Fritz J, Nattestad, Maria, Underwood, Charles J, Fang, Han, Gurtowski, James, Schatz, Michael C

“…GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat…”
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Jasmine and Iris: population-scale structural variant comparison and analysis by Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Battle, Alexis, Aganezov, Sergey, Schatz, Michael C.

“…The availability of long reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through…”
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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome by Goodwin, Sara, Gurtowski, James, Ethe-Sayers, Scott, Deshpande, Panchajanya, Schatz, Michael C, McCombie, W Richard

“…Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a…”
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Big Data: Astronomical or Genomical? by Stephens, Zachary D, Lee, Skylar Y, Faghri, Faraz, Campbell, Roy H, Zhai, Chengxiang, Efron, Miles J, Iyer, Ravishankar, Schatz, Michael C, Sinha, Saurabh, Robinson, Gene E

“…Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data…”
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Hybrid error correction and de novo assembly of single-molecule sequencing reads by 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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A multi-task convolutional deep neural network for variant calling in single molecule sequencing by Luo, Ruibang, Sedlazeck, Fritz J., Lam, Tak-Wah, Schatz, Michael C.

“…The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule…”
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Ribbon: intuitive visualization for complex genomic variation by Nattestad, Maria, Aboukhalil, Robert, Chin, Chen-Shan, Schatz, Michael C

“…Ribbon is an alignment visualization tool that shows how alignments are positioned within both the reference and read contexts, giving an intuitive view that…”
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De Novo Gene Disruptions in Children on the Autistic Spectrum by Iossifov, Ivan, Ronemus, Michael, Levy, Dan, Wang, Zihua, Hakker, Inessa, Rosenbaum, Julie, Yamrom, Boris, Lee, Yoon-ha, Narzisi, Giuseppe, Leotta, Anthony, Kendall, Jude, Grabowska, Ewa, Ma, Beicong, Marks, Steven, Rodgers, Linda, Stepansky, Asya, Troge, Jennifer, Andrews, Peter, Bekritsky, Mitchell, Pradhan, Kith, Ghiban, Elena, Kramer, Melissa, Parla, Jennifer, Demeter, Ryan, Fulton, Lucinda L., Fulton, Robert S., Magrini, Vincent J., Ye, Kenny, Darnell, Jennifer C., Darnell, Robert B., Mardis, Elaine R., Wilson, Richard K., Schatz, Michael C., McCombie, W. Richard, Wigler, Michael

“…Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point…”
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Assembly of large genomes using second-generation sequencing by Schatz, Michael C, Delcher, Arthur L, Salzberg, Steven L

“…Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths,…”
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Quake: quality-aware detection and correction of sequencing errors by Kelley, David R, Schatz, Michael C, Salzberg, Steven L

“…We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and…”
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Sketching and sampling approaches for fast and accurate long read classification by Das, Arun, Schatz, Michael C

“…In modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from…”
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Epigenetic patterns in a complete human genome by 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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Paragraph: a graph-based structural variant genotyper for short-read sequence data by Chen, Sai, Krusche, Peter, Dolzhenko, Egor, Sherman, Rachel M, Petrovski, Roman, Schlesinger, Felix, Kirsche, Melanie, Bentley, David R, Schatz, Michael C, Sedlazeck, Fritz J, Eberle, Michael A

“…Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical…”
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Addressing confounding artifacts in reconstruction of gene co-expression networks by Parsana, Princy, Ruberman, Claire, Jaffe, Andrew E, Schatz, Michael C, Battle, Alexis, Leek, Jeffrey T

“…Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease…”
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