Polyphred vs CodonCode Aligner

[CodonCode]

Just to clarify - CodonCode Aligner is not based on PolyPhred. CodonCode Aligner can be used to view and edit PolyPhred results, but the SNP detection algorithm in CodonCode Aligner was developed independently, and does not use PolyPhred.

The current version of CodonCode Aligner will be useful for gene-by-gene SNP detection and analysis, but not for entire genomes or large chromosomes. Future CodonCode Aligner versions will handle large reference sequences and project better, but for now, Consed/PolyPhred will probably be a better choice.

Cheers,
Peter

[sklages]

I have few hundreds of Sanger sequences. However, I would like to use a genome (735Mb) or a chromosome (~70MB) as a reference sequence. So, I can locate SNPs from different primers and batches to the same reference.

That are not many. That's probably not a problem with either software package.
Are your PCR products (I assume you have PCR products) scattered all over your chromosome? You could use a subsequence of your chromosome and add the truncated sequence offset to your SNP positions.

But, ..we did the mapping itself with consed's "addNewReads" (it uses cross_match); you should give it a try to see if it makes a good job on your 70Mb chromosome. I don't see any problems with the size of your chromosome.

And concerning the commercial packages ... let's give it a try as well.

We exceeded the limits in all our projects with both CCA and Mutation Surveyor, some years ago, things may have changed (or not ;-))

Would be nice to hear feedback on what decisions you have taken and what the results are ..

cheers,
Sven

[shuang]

I have few hundreds of Sanger sequences. However, I would like to use a genome (735Mb) or a chromosome (~70MB) as a reference sequence. So, I can locate SNPs from different primers and batches to the same reference.

[sklages]

We own a license of phred/Phrap/Consed. I'm familiar with Linux.

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. Put together the assembly/alignment process and the SNP calling with polyphred into a "pipeline script". We generated some extra tags for consed to guide the people working with the alignments through some kind of "manual validation" process. 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. Biologists had access to that data via a web interface.

It took some time to write this, we used it quite a few years in production. Still pp v4.x, up to 5.01 AFAIR. I do not have access to the sources anymore ..

You can build whatever you want around the SNP calling itself; that is one advantage over a ready-to-use GUI applications. The disadvantage is that you need to put a lot of work in it ..

On the other hand, download a CCA trial and give it a try. Does it match your needs?
You might want to look at Mutation Surveyor as well; it can analyze something up to 2000 samples at a time (just another limitation the linux programs are lacking).

What dataset sizes we are talking about?

cheers, Sven

[shuang]

We own a license of phred/Phrap/Consed. I'm familiar with Linux.

How complicated it would be to run from the beginning to the end of a SNP discovery?

[sklages]

CodonCode Aligner is based on Polyphred but in a user-friendly interface.

Does Polyphred have any advantage over CodonCode Aligner in turns of functions, abilities, import reference sequence size ...?

We'll use the software in discovering hetero/homo SNPs on Sanger sequences. 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 used polyphred in a home-made SNP-finding/annotating pipeline for PCR-amplified candidate genes together with Consed and friends.

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.

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.

As we just used PCR products (amplicons) as sequencing templates I can't tell you anything about length of sequences in CCA... I am sure Consed/cross_match can deal with very large sequences ...

hth,
Sven

[shuang]

CodonCode Aligner is based on Polyphred but in a user-friendly interface.

Does Polyphred have any advantage over CodonCode Aligner in turns of functions, abilities, import reference sequence size ...?

We'll use the software in discovering hetero/homo SNPs on Sanger sequences. Our office is deciding which one we should purchase.