*2.6.1. Annotation of de novo assembled transcriptome*

In addition to transcriptome abundance calculation after mapping the assembled contigs/ transfragments to the assembled transcriptome or reference genome and differential expres‐ sion data analysis, coding regions within *de novo* assembled transcripts can be searched using ORF predictor tools such as Transdecoder (http://transdecoder.github.io/). Further, homolo‐ gous gene/protein identification of assembled transcripts can be done using tools such as BLAT and BLAST [108].
