I'm currently trying to construct contigs using DNA libraries and am stuck on a particular parameter within the SOAPdenovo2 configuration file. I'm having a hard time understanding what to set "rd_len_cutoff" to. I've read the instructions from the website and they weren't very thorough, at least within my spectrum of understanding. Specifically, the instructions say that rd_len_cutoff tells the assembler what length to cut the reads from the current library to.
How do I determine the ideal length? I apologize if there is already a post that explains this somewhere on here, but I couldn't find one that was more thorough than the source below (I took my time to look before posting).
I also had the same problem for the "rank" parameter.
Thanks for your time!