I am planning to identify SNP within some strains of a nonmodel organism. The organism doesn't have the whole transcriptome sequence identified. So my plan is to make one of the strain's RNA sequence as a reference transcriptome sequence. I have completed the de Novo assembly and now I have around 2000 transcripts(or you can say contigs) for one strain. Can anyone advise me how can I join these transcripts (or RNA contigs) to make a reference RNA sequence?

Thanks in advance!