Work

Back to sequences: Find the origin of k-mers

Year: 2024

Type: article

Abstract: A vast majority of bioinformatics tools dedicated to the treatment of raw sequencing data heavily use the concept of 𝑘-mers, which are words of length 𝑘.This enables us to reduce the redundancy of data (and thus the memory pressure), to discard sequencing errors, and to dispose of objects of fixed size that can be easily manipulated and compared to each other.A drawback is that the link between each 𝑘-mer and the original set of sequences to which it belongs is lost.Given the volume of data considered in this context, recovering this association is costly.In this work, we present "back_to_sequences", a simple tool designed to index a set of 𝑘-mers of interest and to stream a set of sequences, extracting those containing at least one of the indexed 𝑘-mer.In addition, the occurrence positions of 𝑘-mers in the sequences can be provided.Our results show that back_to_sequences streams ≈ 200 short reads per millisecond, allowing to search 𝑘-mers in hundreds of millions of reads in a matter of a few minutes.

Source: The Journal of Open Source Software

DOI: 10.21105/joss.07066

Authors: Anthony Baire, Pierre Marijon, Francesco Andreace, Pierre Peterlongo