SeqWho: reliable, rapid determination of sequence file identity usingk-mer frequencies in Random Forest classifiers

Abstract

Motivation With the vast improvements in sequencing technologies and increased number of protocols, sequencing is being used to answer complex biological problems. Subsequently, analysis pipelines have become more time consuming and complicated, usually requiring highly extensive pre-validation steps. Here we present SeqWho, a program designed to assess heuristically the quality of sequencing files and reliably classify the organism and protocol type by using Random Forest classifiers trained on biases native in k-mer frequencies and repeat sequence identities. Results Using one of our primary models, we show that our method accurately and rapidly classifies human and mouse sequences from nine different sequencing libraries by species, library, and both together, 98.32%, 97.86%, and 96.38% of the time respectively. Ultimately, we demonstrate that SeqWho is a powerful method for reliably validating the quality and identity of the sequencing files used in any pipeline. Availability https://github.com/DaehwanKimLab/seqwho Supplementary information Supplementary data are available at Bioinformatics online.