After SNP/INDELs have been confirmed (or created) in consed via some specfic tags, we have parsed the ACE file for such tags and put the results together with some statistics in a database. We generated some extra tags for consed to guide the people working with the alignments through some kind of "manual validation" process. Put together the assembly/alignment process and the SNP calling with polyphred into a "pipeline script". How complicated it would be to run from the beginning to the end of a SNP discovery?AFAIK there is no out-of-the-box solution. I am sure Consed/cross_match can deal with very large sequences. If you just want to analyze your data very quickly with a nice interface (not running in a linux environment), you'd probably go for CodonCode Aligner.Īs we just used PCR products (amplicons) as sequencing templates I can't tell you anything about length of sequences in CCA. If you have a large amount of sanger data, some programming skills, an affinity for linux and little bit of spare time, it is probably not a very good option. We used polyphred in a home-made SNP-finding/annotating pipeline for PCR-amplified candidate genes together with Consed and friends. Our office is deciding which one we should purchase.Polyphred is not very useful as stand-alone program out-of-the-box instead it works tightly integrated with phred/Phrap/Consed (which are the powerful Unix pendants to CCA). We'll use the software in discovering hetero/homo SNPs on Sanger sequences. CodonCode Aligner is based on Polyphred but in a user-friendly interface.ĭoes Polyphred have any advantage over CodonCode Aligner in turns of functions, abilities, import reference sequence size.
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