kmindex

kmindex indexes and queries sequencing samples to enable rapid sequence searches across large-scale genomic datasets.

Key Features:

• Scalable indexing: kmindex can index thousands of metagenomes with construction speed an order of magnitude faster than previous methods.
• Ultra-fast querying: kmindex performs sequence searches in a fraction of a second, with search times two orders of magnitude faster than existing approaches.
• High precision: kmindex achieves negligible false positive rates below 0.01%, outperforming existing approaches by four orders of magnitude.
• Large-scale demonstration: kmindex successfully indexed 1,393 marine seawater metagenome samples from the Tara Oceans project.

Scientific Applications:

• Metagenomic database search: kmindex enables efficient searching of public sequencing databases for any sequence(s) of interest.
• Ocean metagenomics: kmindex supports large-scale marine microbial community analysis through indexing and querying of oceanic metagenome collections.

Methodology:

kmindex is built on top of kmtricks.