sangerFlow, a Sanger sequencing-based bioinformatics pipeline for pests and pathogens identification

Abstract

Sequencing of a Polymerase Chain Reaction product (amplicon) is called amplicon sequencing. Amplicon sequencing allows for reliable identification of an organism by amplifying, sequencing, and analysing a single conserved marker gene or DNA barcode. As this approach generally involves a single gene, it is a light-weight protocol compared to multi-locus or whole genome sequencing for diagnostic purposes; yet considerably reliable. Therefore, Sanger-based high-quality amplicon sequencing is widely deployed for species identification and high-throughput biosecurity surveillance. However, keeping up with the data analysis in a large-scale surveillance or diagnostic settings could be a limiting factor because it involves manual quality control of the raw sequencing data, alignment of the forward and reverse reads, and finally web-based Blastn search of all the amplicons. Here, we present a bioinformatics pipeline that automates the entire analysis. As a result, the pipeline is scalable with high-volume of samples and reproducible. Furthermore, the pipeline leverages the modern open-source Nextflow and Singularity concept, thus it does not require software installation except Nextflow and Singularity, software subscription, or programming expertise from the end users making it widely adaptable. Availability and implementationsangerFlow source code and documentation are freely available for download at GitHub, implemented in Nextflow and Singularity.