summary.seqs takes ages

I am analysering 96 samples. I made the contigs using mothur and it went throught. Now I would like to see the summary of seqs using summary.seqs, for several times, I have put the job on the server with 12 cores, but has not got the result yet !

my coworkers says, there are too many unique sequences and that’s why it takes so much time. I was wondering if there is any tip or if I can use other assembly methods I should use ? ( I am using the latest version of mothur on linux)

What classifies as taking ages?

Have you seen this?

Thanks for addressing the paper.

  1. My PI has sequenced V3-V4 regions and he is saying there is a big overlap on pair end sequencing (first I don’t know how to double check it by myself to see how much of pairs over lap!).

  2. How can I evaluate the quality of contigs ! sorry this might sounds like an open question so pleae feel free to address a paper or …

  3. so, if the pairs overlap is good enough and the contig quality is good as well, taking ages (making contig within 24 hours under 12 cores) is natural then !

The point of this link…

… and this paper …

… is that the V3-V4 reads will not overlap adequately.