Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA
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| Format: | Preprint |
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2025
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| author | Ghosh, Priyanka Fagnan, Kjiersten Connor, Ryan Pannu, Ravinder Wheeler, Travis J. Pop, Mihai Brown, C. Titus Pierce-Ward, Tessa Patro, Rob Michaelis, Jacquelyn S. Madden, Thomas L. Camacho, Christiam Awe, Olaitan I. Krinos, Arianna I. Xavier, René KM Polo, Rodrigo Ortega Roddy, Jack W. Rhodes, Adelaide Sweeten, Alexander Viehweger, Adrian Ekim, Bariş Muralidharan, Harihara Subrahmaniam Rahman, Amatur Salazar, Vinícius W. Tritt, Andrew Colligan, Thomas Kalantar, Katrina Krause, Genevieve R. Reiter, Taylor Lesica, George Babaian, Artem Lin, Victor Madaminov, Sergey Zalunin, Vadim Kristensen, David M. Salsbury, Alexa Rice, Daniel P. Brister, J. Rodney |
| author_facet | Ghosh, Priyanka Fagnan, Kjiersten Connor, Ryan Pannu, Ravinder Wheeler, Travis J. Pop, Mihai Brown, C. Titus Pierce-Ward, Tessa Patro, Rob Michaelis, Jacquelyn S. Madden, Thomas L. Camacho, Christiam Awe, Olaitan I. Krinos, Arianna I. Xavier, René KM Polo, Rodrigo Ortega Roddy, Jack W. Rhodes, Adelaide Sweeten, Alexander Viehweger, Adrian Ekim, Bariş Muralidharan, Harihara Subrahmaniam Rahman, Amatur Salazar, Vinícius W. Tritt, Andrew Colligan, Thomas Kalantar, Katrina Krause, Genevieve R. Reiter, Taylor Lesica, George Babaian, Artem Lin, Victor Madaminov, Sergey Zalunin, Vadim Kristensen, David M. Salsbury, Alexa Rice, Daniel P. Brister, J. Rodney |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2505_06395 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA Ghosh, Priyanka Fagnan, Kjiersten Connor, Ryan Pannu, Ravinder Wheeler, Travis J. Pop, Mihai Brown, C. Titus Pierce-Ward, Tessa Patro, Rob Michaelis, Jacquelyn S. Madden, Thomas L. Camacho, Christiam Awe, Olaitan I. Krinos, Arianna I. Xavier, René KM Polo, Rodrigo Ortega Roddy, Jack W. Rhodes, Adelaide Sweeten, Alexander Viehweger, Adrian Ekim, Bariş Muralidharan, Harihara Subrahmaniam Rahman, Amatur Salazar, Vinícius W. Tritt, Andrew Colligan, Thomas Kalantar, Katrina Krause, Genevieve R. Reiter, Taylor Lesica, George Babaian, Artem Lin, Victor Madaminov, Sergey Zalunin, Vadim Kristensen, David M. Salsbury, Alexa Rice, Daniel P. Brister, J. Rodney Other Quantitative Biology 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. |
| title | Contributions of the Petabyte Scale Sequence Search Codeathon toward efforts to scale sequence-based searches on SRA |
| topic | Other Quantitative Biology |
| url | https://arxiv.org/abs/2505.06395 |