Dataset Information

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

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.

SUBMITTER: Bonenfant Q

PROVIDER: S-EPMC9869717 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

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

Bonenfant Quentin Q Noé Laurent L Touzet Hélène H

Bioinformatics advances 20221121 1

<h4>Motivation</h4>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 ...[more]

PMID: 36698762

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Dataset Information

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

Motivation

Results

Availability and implementation

Supplementary information

Publications

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

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