I have single ended transcriptome data generated in ion torrent platform. in which i want to perform transcriptome assembly using trinity. i have tried so many time, trinity tool take too much time and the job status indicated " this job is waiting to run". No further process is operated. can you please give me alternative to trinity de novo assembler for ion torrent dataset?
jobs can be delayed when the Galaxy servers are under heavy load. Also, launching multiple jobs or deleting queued jobs then rerun new ones can also cause delays. I recommend you launch the analysis again when the server is under less load (you can check the European server status here).
On the other hand, as an alternative tool, you can use Spades.