**Annotation**

Resulting contigs were compared to the Uniprot/Swiss-Prot protein database using BLASTx using the following parameters: an evalue threshold of 1e-05, one sequence match and one sequence per contig. Blastx results were merged with SPID and GO Numbers databases (citation [don't know the source of these databases]). Biological Process GO-slim parameters were used in order to summarize annotation. 

Interested particularly on genes involved in reproductive biology, we examined the transcriptome for previously described gene sets. One suite of genes previoiusly characterized is from Dheilly et al 2012 where researchers described sex and stage specific genes in _Crassostrea gigas_.  To make this comparison, the fasta file corresponding to the Dheilly study microarray study (available from Olson and Roberts, 2014) was compared to the Panopea transcriptome using Blastn (evalue 1e-60) and SQLShare used to join with Dheilly et al 2012 supplemental table 1 (sex-specific genes)  and supplemental table 2 (gametogenesis differential expression).