kmindex and ORA: indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets

Abstract

AbstractPublic sequencing databases contain vast amounts of biological information, yet they are largely underutilized as one cannot efficiently search them for any sequence(s) of interest. We presentkmindex, an innovative approach that can index thousands of highly complex metagenomes and perform sequence searches in a fraction of a second. The index construction 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%,kmindexoutperforms the precision of existing approaches by four orders of magnitude. We demonstrate the scalability ofkmindexby successfully indexing 1,393 complex marine seawater metagenome samples from theTaraOceans project. Additionally, we introduce the publicly accessible web server “Ocean Read Atlas” (ORA) athttps://ocean-read-atlas.mio.osupytheas.fr/, which enables real-time queries on theTaraOceans dataset. The open-sourcekmindexsoftware is available athttps://github.com/tlemane/kmindex.