I want to assembly a genome generated from HiSeq 2x250 bp with 350 bp insert size. I usually use SPAdes for assembly, but I just found out that SPAdes suggests using 550-700 bp fragments with 2x250 reads. May I ask if you have experience using SPAdes with 2x250 on 350 insert size? Is it just fine to use it or shall I use another tool?
Thanks in advance and have a great weekend!