TSETA (Third-generation Sequencing to Enable Tetrad Analysis) is a fungus-centric software pipeline that utilizes chromosome-level sequence assembly for genome-wide and single-nucleotide-resolution mapping of single-nucleotide polymorphisms (SNPs), meiotic recombination products, illegitimate mutations (IMs) and repeat-induced point (RIP) mutations. It utilizes a newly invented algorithm (i.e., BLASTN-guided sectional MAFFT) to perform fast, accurate, and low-cost multiple genome sequence alignments. This new algorithm outcompetes next-generation sequencing (NGS)-based variant-calling approaches for accurate and comprehensive identification of single-nucleotide variants (SNVs) and insertion/deletion mutations (Indels) among the near-complete genome sequences of any two or more intraspecific strains, as well as sequences before and after meiosis, with single-nucleotide precision. TSETA also has a powerful tool for the visualization of the results from the scale of the chromosomal landscape to individual nucleotides. The data output files are user-friendly for researchers and students lacking computational expertise to analyze and reason about data and evidence.
Keywords: CBS999.97(MAT1-1); Chromosome-level genome sequences; Meiotic recombination products; PacBio long-read sequencing; QM6a; Repeat-induced point mutation; SNP calling; Third-generation sequencing; Trichoderma reesei.