I wonder if anyone has tried to chain up mothur and assembly for 454 sequences? Mothur has all those sequence trimming and quality checking functions that are very useful. So my idea is to use mothur to quality check my raw sff and then send the results to assemblers such as MIRA or Newbler?
As far as I know, MIRA needs three files to operate: fasta, fasta.qual and TRACEINFO xml. All of them can be extracted by sff_extract from the raw sff data. But after I trim.flow and shhh.flow my sff, I have a fasta file that is good to use. The qual file from shhh.flow is not the fasta.qual MIRA wants, so how can I have the fasta.qual instead? And how can I generate TRACEINFO.xml from the shhh.flow output?
Thank you in advance.