SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species
(a) SNiPloid procedure. For each reference sequence or gene of a diploid genome G2, SNiPloid extracts intervals that meet a minimal coverage depth threshold for each sample (1a) and identify overlapping intervals between samples (1b). It then extracts putative SNPs in both samples within these defined common regions (2) and compares the differences observed between samples in order to interpret the situation (3). (b) Phylogenetic contexts within a polyploidy genome and assignment of SNP categories.
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