Development and Evaluation of an MLSA-ONT Barcoding Workflow for the Diagnosis of 'Candidatus Phytoplasma'

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. Preparation_scripts alignment_and_distance_matrix_from_fasta.R : this R script reads a file in fasta format, aligns the sequences, calculates pairwise distances and generates a heatmap-like figure. primer_evaluation.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. Reference_databases RefSeq_Phytoplasma_XXX.fasta : fasta files with the reference sequences of the different barcodes used in the study. RefSeq_Phytoplasma_XXX_sintax.fasta : fasta files with the reference sequences of the different barcodes used in the study in sintax format, necessary for read-based taxonomic assignment. heatmap_sim_XXX_Phytoplasma_ref_seqs_from_literature.pdf : pairwise similarity matrices (in the form of a heatmap) of the reference sequences of the different barcodes used in the study. Pipeline_scripts : scripts used in the data analysis pipeline.