Additional file 1 of MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

Tables S1-S15. Microsoft Excel Workbook containing 15 worksheets. Table S1: Description of Pst isolates. Table S2: Number of reads aligned to the PST-130 reference genome for the 100 RNA-seq datasets. Table S3: Number of reads aligned to the PST-130 reference genome for the 25 genomic datasets utilised herein. Table S4: Oligonucleotide (primer) sequences and pooling strategy for the 242 Pst genes selected. Table S5: Genomic location and functional annotation of the 242 Pst genes selected. Table S6: Number of reads aligned to the PST-130 reference genome for the 4 MiSeq amplicon datasets. Table S7: Number of reads generated on the MinION platform that aligned to the 242 Pst genes selected. Table S8: Time taken to generate a given number of MinION reads for the four Ethiopian Pst-infected wheat samples. Table S9: Details of SNP positions per gene detected in MinION and Illumina datasets generated from four Pst isolates. Table S10: Details of homokaryotic and heterokaryotic positions in consensus sequences obtained from Illumina MiSeq and MinION platforms. Table S11: Number of reads aligned to the PST-130 reference genome for the Ethiopian Pst RNA-seq datasets. Table S12: Additional Pst reference isolates representing diverse virulence phenotypes and key genetic groups of a worldwide phylogeny of Pst. Table S13: Components used in the MARPLE pipeline. Table S14: Details of Illumina library preparation of 4 Pst-infected samples. Table S15: Details of libraries made for MinION sequencing of Pst-infected wheat leaf samples. (XLSX 4138 kb)