I have assembled a de novo transcriptome from my species of interest. The species has an internal symbiont (algae) and those sequences obviously we sequenced along with it. I have done a blast on my assembly which has ID'd a number of contigs corresponding to the symbiont. I would like to use the results of the blast to remove those contigs from the assembly into a new file so I can deal with the two organisms separately. It there an easy way to do this?
The assembly contains ~350,000 contigs.