[Biopython] sff inot fasta and qual then trim

Kiss, Csaba csaba.kiss at lanl.gov
Tue Oct 23 20:32:11 UTC 2012


>That sounds a bit slow, can you compare this to the Biopython SFF conversion time (or any of the other tools)?
I used 
SeqIO.convert("sd6.sff", "sff-trim", "sd6_p.fasta", "fasta")
SeqIO.convert("sd6.sff", "sff-trim", "sd6_p.qual", "qual")

and it finished in 8 minutes. That's much better than 3 hours. The problem is that if I use the mothur fasta/qual files and the python fasta/qual files and trim the sequences exactly the same way in mothur, I get slightly different trimmed sequence dataset.
I am investigating further, if it would matter.
Thanks for your helps, it is much appreciated
Csaba




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