Back to sequences: find the origin ofk-mers

Abstract

AbstractA vast majority of bioinformatics tools dedicated to the treatment of raw sequencing data heavily use the concept ofk-mers. This enables us to reduce the data redundancy (and thus the memory pressure), to discard sequencing errors, and to dispose of objects of fixed size that can be manipulated and easily compared to each others. A drawback is that the link between eachk-mer and the original set of sequences it belongs to is generally lost. Given the volume of data considered in this context, finding back this association is costly. In this work, we present “back_to_sequences”, a simple tool designed to index a set ofk-mers of interests, and to stream a set of sequences, extracting those containing at least one of the indexedk-mer. In addition, the number of occurrences ofk-mers in the sequences is provided. Our results show thatback_to_sequencesstreams≈200 short read per millisecond, enabling to searchk-mers in hundreds of millions of reads in a matter of a few minutes.Availabilitygithub.com/pierrepeterlongo/back_to_sequences