Strategies for genome-specific assembly and annotation of the tetraploid wheat transcriptome. (A) Overall assembly pipeline. Functional steps are listed on the left and specific programs used for each step on the right. Programs developed during the course of this study are underlined. (B) Steps used in the annotation. (C) Post-assembly processing pipeline using phasing to separate homoeolog-specific sequences. (D) Illustration of the phasing process. Reads are re-aligned to the reference transcriptome, single nucleotide polymorphisms (SNPs) between homoeologs are identified (in red), and phased. The example shows the phasing of A and C SNPs at positions 5 and 16 in phase 0 and G and T SNPs in phase 1.
Krasileva et al. Genome Biology 2013 14:R66 doi:10.1186/gb-2013-14-6-r66