REINDEER

efficient indexing of k-mer presence and abundance in sequencing datasets. REINDEER builds a data-structure that indexes k-mers and their abundances in a collection of datasets (raw RNA-seq or metagenomic reads for instance). Then, a sequence (FASTA) can be queried for its presence and abundance in each indexed dataset. While other tools (e.g. SBT, BIGSI) were also designed for large-scale k-mer presence/absence queries, retrieving abundances was so far unsupported (except for single datasets, e.g. using some k-mer counters like KMC, Jellyfish). REINDEER combines fast queries, small index size, and low memory footprint during indexing and queries. We showed it allows to index 2585 RNA-seq datasets (~4 billions k-mers) using less than 60GB of RAM and a final index size lower than 60GB on the disk. Then, a REINDEER index can either be queried on disk (experimental feature, low RAM usage) or be loaded in RAM for faster queries.