ntEmbd: Deep learning embedding for nucleotide sequences

Enabled by the explosion of data and substantial increase in computational power, deep learning has transformed fields such as computer vision and natural language processing (NLP) and it has become a successful method to be applied to many transcriptomic analysis tasks. A core advantage of deep learning is its inherent capability to incorporate feature computation within the machine learning models. This results in a comprehensive and machine-readable representation of sequences, facilitating the downstream classification and clustering tasks. Compared to machine translation problems in NLP, feature embedding is particularly challenging for transcriptomic studies as the sequences are string of thousands of nucleotides in length, which make the long-term dependencies between features from different parts of the sequence even more difficult to capture. This highlights the need for nucleotide sequence embedding methods that are capable of learning input sequence features implicitly. Here we introduce ntEmbd, a deep learning embedding tool that captures dependencies between different features of the sequences and learns a latent representation for given nucleotide sequences. We further provide two sample use cases, describing how learned RNA features can be used in downstream analysis. The first use case demonstrates ntEmbd's utility in classifying coding and noncoding RNA benchmarked against existing tools, and the second one explores the utility of learned representations in identifying adapter sequences in nanopore RNA-seq reads. The tool as well as the trained models are freely available on GitHub at https://github.com/bcgsc/ntEmbd.