QC with trim.seqs before make.contigs


I know it’s not the way described in the MiSeq pipeline, but I’m trying to make a selection of good quality sequences right at the beginning. As I can see using fastQC, my fastq sequences don’t have a really good quality so I’d like to trim them before combining paired reads using make.contigs.
Trim.seqs offers the possibility to trim according to the quality scores, so that’s why I want to use it as a first step (after that we’re using fasta files, so we loose the quality scores; or we just can’t use the qfiles generated by make.contigs). So I did, and I observed a rise in quality scores and that’s what I wanted. The problem is making contigs out of theses files, it does not work. I received two kinds of error :

1)[WARNING]: name mismatch in forward quality file. Ignoring _______


  1. ______ is in your forward fasta file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
    Making contigs…
    Segmentation fault (core dumped)

It looks like forward and reverse files are not compatible anymore. Is there any way I can solve this or I don’t have any other possibility than beginning with make.contigs? I want to do this because I can see the quality of the sequences and correct when needed; I can’t with make.contigs…
Thanks a lot for your help

When we’ve tried this in the past with mock community data (so we actually know what we’re measuring) pre-trimming does not improve the assembly.