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- W4379379188 abstract "Abstract Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as one cannot efficiently search them for any sequence of interest. We present kmindex , an innovative approach that can index thousands of highly complex metagenomes and perform sequence searches in a fraction of a second. The construction of the index is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. We demonstrate the scalability of kmindex by successfully indexing 1,393 complex marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server “Ocean Read Atlas” ( ORA ) at https://ocean-read-atlas.mio.osupytheas.fr/ , which enables real-time queries on the entire Tara Oceans dataset. The open-source kmindex software is available at https://github.com/tlemane/kmindex ." @default.
- W4379379188 created "2023-06-06" @default.
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- W4379379188 date "2023-06-04" @default.
- W4379379188 modified "2023-09-30" @default.
- W4379379188 title "kmindex and ORA: indexing and real-time user-friendly queries in terabytes-sized complex genomic datasets" @default.
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- W4379379188 doi "https://doi.org/10.1101/2023.05.31.543043" @default.
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