This Zenodo repository contains materials associated with the paper "Development and Evaluation of an MLSA-ONT Barcoding Workflow for the Diagnosis of ‘Candidatus Phytoplasma’" in the journal PhytoFrontiers. The following information is included: README file in markdown format explaining the contents of the repository and an explanation of the different steps in the bioinformatics data analysis pipeline. Preparationₛcripts alignmentₐnddistanceₘatrixfromfasta. R: this R script reads a file in fasta format, aligns the sequences, calculates pairwise distances and generates a heatmap-like figure. primerₑvaluation. R: this R script reads a fasta file with sequences and a fasta file with primers. It will look for primer matches in each sequence, it will extract the primer matches and align them, and make a sequence logo. The script outputs an alignment of the extracted primer matches, a position frequency matrix showing the relative occurrence of the bases at each position of the primer, a list with the number of primer mismatches per sequence and a visual representation under the form of a sequence logo. Referencedatabases RefSeqPhytoplasmaXXX. fasta: fasta files with the reference sequences of the different barcodes used in the study. RefSeqPhytoplasmaXXXₛintax. fasta: fasta files with the reference sequences of the different barcodes used in the study in sintax format, necessary for read-based taxonomic assignment. heatmapₛimXXXPhytoplasmaᵣefₛeqsfromₗiterature. pdf: pairwise similarity matrices (in the form of a heatmap) of the reference sequences of the different barcodes used in the study. Pipelineₛcripts: scripts used in the data analysis pipeline.
Everaert et al. (Mon,) studied this question.