Dear Friends,
I need a help. I have 30 paired end reads of 30 samples and I need to assemble it in a single go using SOAPdenovo with a single command. I have already done it one by one but I need a command to perform all the 30 read files at once.
Thank you Michael
Why is this a
blog
type post? Please read: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and BookmarkingTried anything like looping, GNU parallel or the like?
Do you want a single assembly using all 30 samples as input? Or do you want 30 assemblies, but all running in parallel?
try to follow soapdenovo2 manual here: https://hcc-docs.unl.edu/display/HCCDOC/SOAPdenovo2. For paired end, you can create one single config file and submit it to cluster. Example script is furnished in the manual.