I am in the process of cobbling together a NGS pipeline for trimming, assembling, and annotating genomes for our group and I also have very limited bioinformatics experience. I would like to be able to run several SPAdes jobs at once. Thankfully, I have access to a cluster that uses SGE. However, I have been unable to set-up an array job with SPAdes. The SPAdes command line interface keeps trying to read the index variable needed for SGE to run an array as part of the file name, which it then can't find. I tried concatenating my files and having one entry per line, but that also has failed. Any suggestions so as to avoid writing the same thing over and over again on the command line with only slight changes in the input file name?