Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming

Abstract

Abstract Motivation Oxford Nanopore Technologies (ONT) sequencing has become very popular over the past few years and offers a cost-effective solution for many genomic and transcriptomic projects. One distinctive feature of the technology is that the protocol includes the ligation of adapters to both ends of each fragment. Those adapters should then be removed before downstream analyses, either during the basecalling step or by explicit trimming. This basic task may be tricky when the definition of the adapter sequence is not well documented. Results We have developed a new method to scan a set of ONT reads to see if it contains adapters, without any prior knowledge on the sequence of the potential adapters, and then trim out those adapters. The algorithm is based on approximate k-mers and is able to discover adapter sequences based on their frequency alone. The method was successfully tested on a variety of ONT datasets with different flowcells, sequencing kits and basecallers. Availability and implementation The resulting software, named Porechop_ABI, is open-source and is available at https://github.com/bonsai-team/Porechop_ABI. Supplementary information Supplementary data are available at Bioinformatics advances online.