The repository extensively utilizes Biopython to conduct local blast searches and search NCBI databases. For those not familiar with Biopython we highly recommend it for general bioinformatics usage. Software utilized for transcriptome assembly and annotation.
It was the primary software used transcriptome assembly. Unless indicated, Trinity was not set to exclude small assembled contigs to allow for future discovery by end-users.
Blast2Go and CLC Genomics Workbench were used in some annotation and assembly, however due to the cost of these software they were only used sparingly.