Autoplay Next video from Max length

CppCon 2014: Mauricio Carneiro "Gamgee: A C++14 library for genomics data processing and analysis"

2,294 views · Published 23 October 2014 · 1:08:02 · Indexed 30 September 2026

Channel: CppCon · 2014 · Education

http://www.cppcon.org
—
Presentation Slides, PDFs, Source Code and other presenter materials are available at: https://github.com/CppCon/CppCon2014
--
Our group has defined the standards for DNA and RNA sequencing data processing and analysis for disease research and clinical applications. In the last 5 years we have published our tools in the GATK (genome analysis toolkit) which is completely written in java. With the scaling of next generation sequencing and the immense amount of that needs to be processed we hit a performance wall and found ourselves limited by the language to make optimizations and rewrite the algorithms in a way that would conform better to modern hardware.

Enter Gamgee. A free and open source C++14 library that offers much of the functionality of the GATK framework with the performance necessary to scale to the hundreds of petabytes of todays complex diseases projects. We will show how the tools developed using the Gamgee library replaced legacy java GATK tools in the production pipeline of the Broad Institute. We will also talk about how the algorithms have changed to take advantage of the native libraries and modern hardware features such as SSE/AVX and GPUs.
--
Dr. Carneiro leads the computational technology development team at the Broad Institute of MIT and Harvard. He has contributed to major advances in DNA sequencing analysis with compression algorithms, statistical methods, heterogeneous compute optimizations and a systematic approach to the institute's computational development, distribution and support. His team is also responsible for the evaluation of new sequencing technologies and has provided several methods and tools to handle new data types in the world of next generation sequencing through the Genome Analysis Toolkit (GATK).Dr. Carneiro joined the Broad Institute in December 2010 after completing a Ph.D. in computational biology from Harvard University. He holds two championships in the International Collegiate Programming Contest organized by the Association for Computing Machinery (ACM) in 2002 and 2003, respectively, and a Programming Excellence Award from the ACM Upsilon Pi Epsilon Society in 2003.In his previous life, he was a video game developer and has led the development of the world's first massive online location based multiplayer game: Alien Revolt.Website: http://www.broadinstitute.org/~carneiro/Twitter handle: @Mauricinho
--
Videos Filmed & Edited by Bash Films: http://www.BashFilms.com

Work at Hudson River Trading (HRT): https://tinyurl.com/safxfctf

CppCon 2014: Mauricio Carneiro "Gamgee: A C++14 library for genomics data processing and analysis"

More from this channel