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• W3124173881 abstract "Abstract Background The need to associate information to words is shared among a plethora of applications and methods in high throughput sequence analysis, and could be marked as fundamental. A scalability problem is promptly met when indexing billions of k-mers, as exact associative indexes can be memory expensive. To leverage this challenge, recent works take advantage of the k-mer sets properties. They exploit the overlaps shared among k-mers by using a De Bruijn graph as a compact k-mer set to provide lightweight structures Contribution We propose a scalable and exact index structure able to associate unique identifiers to indexed k-mers and to reject alien k-mers. The proposed index combines an extremely compact representation along with a high throughput. Moreover, it can be efficiently built from the De Bruijn graph sequences. The efficient index implementation we provide, achieved to index the k-mers from the human genome with 8GB within 30 minutes and was able to scale up to the huge axolotl genome with 63 GB within 10 hours. Furthermore, while being memory efficient, the index allows above a million queries per second on a single CPU in our experiments and its throughput can be raised using multiple cores. Finally, we also present the index ability to practically represent metagenomic and transcriptomic sequencing data to highlight its wide applicative range. Availability The index is implemented as a header-only library in C++, is open source under AGPL3 license and available at https://github.com/Malfoy/Blight. It was designed as a user-friendly library and comes along with sample code usage." @default.
• W3124173881 created "2021-02-01" @default.
• W3124173881 creator A5001793115 @default.
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• W3124173881 creator A5050139327 @default.
• W3124173881 date "2019-02-11" @default.
• W3124173881 modified "2023-09-23" @default.
• W3124173881 title "Indexing De Bruijn graphs with minimizers" @default.
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• W3124173881 hasPublicationYear "2019" @default.
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