Find paralogs in a draft genome We generated a (diploid, chordata, highly heterozgous) genome using PacBio and we wanted to see whether it contains lineage-specific duplications (paralogs, basically). The genome is not in Ensembl yet. 

The only data we have at the moment are:


genome
transcript annotation
RNAseq 


We found some methods from papers:


use Blast
detect segmental duplications in complete genomes with SDDdetector
detecting putative recent segmental duplications or diploid homozygous organisms based on NGS data DuplicationDetector
(I just came up with this, but should work) map back the reads to the assembly &amp; analyze the read depth to detect duplicated portions


I'll gladly take advice.
This is really tough to do with highly heterozygous animals. What are your genome assembly stats? Specifically, what is your number of contigs, scaffolds, assembly size, and the N50?

If you have proximity ligation data it will be easier to determine if potential paralogs are truly from different regions of the genome or are just from homologous locations on sister chromatids that ended up in uncollapsed in your final assembly.

If I were you and had a good genome, I would start by annotating gene models using RNAseq data, then blasting each gene in the model against all genes in the model. This would give you potential paralogs to start looking at more closely.