how to use make.contigs

Hi, thank you for help in advance. I have say 50 samples, with multiple pairs of FASTQ files for each sample. My questions are:

  1. Can I process 50 samples separately in mother following the MiSeq SOP? I mean, can I run 50 separate jobs for 50 samples? I think I can do so if there are no steps in mothur where reads from different samples are pooled (like the GATK use pooled reads to call variants sites).
  2. For one sample that has say 5 pairs of fastq files, can I run make.contigs 5 times for each pairs of FASTQ files to use 5 CPU cores at the same time? If yes, how can I merge them later?
    Thanks a lot.

In the file you give make.contigs you can give multiple pairs of files the same group name and then those sequences will be pooled together into the same group.

I think that’s what you’re after…