Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA
Abstrak
The volume of biological data being generated by the scientific community is growing exponentially, reflecting technological advances and research activities. The National Institutes of Health's (NIH) Sequence Read Archive (SRA), which is maintained by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), is a rapidly growing public database that researchers use to drive scientific discovery across all domains of life. This increase in available data has great promise for pushing scientific discovery but also introduces new challenges that scientific communities need to address. As genomic datasets have grown in scale and diversity, a parade of new methods and associated software have been developed to address the challenges posed by this growth. These methodological advances are vital for maximally leveraging the power of next-generation sequencing (NGS) technologies. With the goal of laying a foundation for evaluation of methods for petabyte-scale sequence search, the Department of Energy (DOE) Office of Biological and Environmental Research (BER), the NIH Office of Data Science Strategy (ODSS), and NCBI held a virtual codeathon 'Petabyte Scale Sequence Search: Metagenomics Benchmarking Codeathon' on September 27 - Oct 1 2021, to evaluate emerging solutions in petabyte scale sequence search. The codeathon attracted experts from national laboratories, research institutions, and universities across the world to (a) develop benchmarking approaches to address challenges in conducting large-scale analyses of metagenomic data (which comprises approximately 20% of SRA), (b) identify potential applications that benefit from SRA-wide searches and the tools required to execute the search, and (c) produce community resources i.e. a public facing repository with information to rebuild and reproduce the problems addressed by each team challenge.
Topik & Kata Kunci
Penulis (38)
Priyanka Ghosh
Kjiersten Fagnan
Ryan Connor
Ravinder Pannu
Travis J. Wheeler
Mihai Pop
C. Titus Brown
Tessa Pierce-Ward
Rob Patro
Jacquelyn S. Michaelis
Thomas L. Madden
Christiam Camacho
Olaitan I. Awe
Arianna I. Krinos
René KM Xavier
Rodrigo Ortega Polo
Jack W. Roddy
Adelaide Rhodes
Alexander Sweeten
Adrian Viehweger
Bariş Ekim
Harihara Subrahmaniam Muralidharan
Amatur Rahman
Vinícius W. Salazar
Andrew Tritt
Thomas Colligan
Katrina Kalantar
Genevieve R. Krause
Taylor Reiter
George Lesica
Artem Babaian
Victor Lin
Sergey Madaminov
Vadim Zalunin
David M. Kristensen
Alexa Salsbury
Daniel P. Rice
J. Rodney Brister
Akses Cepat
- Tahun Terbit
- 2025
- Bahasa
- en
- Sumber Database
- arXiv
- Akses
- Open Access ✓