10 individuals (samples) will be pooled and normalized into a single library for transcriptome sequencing. The reads will be paired-end and 85bp in length.
This is a non-model plant organism (so no close relative for alignment purposes).
Is this design the best strategy for SNP detection? (should barcoding and multi-plexing be employed?)
What are the best tools for SNP detection in this design (de novo assembly with a tool such as Velvet will be necessary and then?)