I have gotten 25 MiSeq, single read fasta files from my collaborators to analyse. I wish to combine them and run as a group, as mentioned in the SOP. The make.contigs command does not seem to work for me. I tried the merge.files command, but there is no .group file that lists the individual fasta files. Is there other command to do that?
And if I have 10 files that are labeled Test1.fasta to Test10.fasta, how do I name or loop them in a batch file so I will be able to run them without listing all the commands for each fasta?