T
Thomas William
Researcher at Dresden University of Technology
Publications - 16
Citations - 6849
Thomas William is an academic researcher from Dresden University of Technology. The author has contributed to research in topics: Lustre (file system) & Wide area network. The author has an hindex of 6, co-authored 16 publications receiving 5495 citations.
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Journal ArticleDOI
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +22 more
TL;DR: This protocol describes the use of the Trinity platform for de novo transcriptome assembly from RNA-Seq data in non-model organisms and presents Trinity’s supported companion utilities for downstream applications, including RSEM for transcript abundance estimation and R/Bioconductor packages for identifying differentially expressed transcripts across samples.
Book ChapterDOI
BenchIT — Performance measurement and comparison for scientific applications
Guido Juckeland,S. Börner,Michael Kluge,S. Kölling,Wolfgang E. Nagel,Stefan Pflüger,H. Röding,Stephan Seidl,Thomas William,R. Wloch +9 more
TL;DR: The BenchIT-project provides such an evaluation platform by offering a variety of measurement kernels, as well as a easily accessible plotting engine, thus enabling an easy way to measure performance on a specific system and compare the result, which is a full graph instead of just a number, to other results contributed by other users.
Proceedings ArticleDOI
Demonstrating lustre over a 100Gbps wide area network of 3,500km
Robert Henschel,Stephen C. Simms,David Y. Hancock,Scott Michael,Tom Johnson,Nathan Heald,Thomas William,Don Berry,Matthew R. Allen,Richard Knepper,Matthew Davy,Matthew R. Link,Craig A. Stewart +12 more
TL;DR: The configuration and constraints of the Lustre high performance parallel file system demonstration are described and key findings are outlined.
Posted ContentDOI
The Impact of High-Performance Computing Best Practice Applied to Next-Generation Sequencing Workflows
Pierre Carrier,Bill Long,Walsh R,Dawson J,Carlos P. Sosa,Brian J. Haas,Timothy L. Tickle,Thomas William +7 more
TL;DR: This study describes how distributed-memory parallelism can be an important enhancement to the performance and resource utilization of NGS workflows, and shows results on the parallelization of the Inchworm module of the Trinity RNA-Seq pipeline for de novo transcriptome assembly.