staden gap4 versus phrap/consed (instead of sequencher)
I've got the STADEN suite running with PHRAP. Using pregap4 > gap4 I have been able to assemble small groups of .abi trace files into contigs very easily, then edit them and output the consensus. It runs very nicely on 10.4.x and is as good as Sequencher although the initial setup (compiling, setting environmental variables) requires a working knowledge of unix. I can get two overlapping .abi files assembled and be editing the contig (with aligned chromatogram files) in about 30 seconds in gap4.
Next, I thought I'd check out the phred/phrap/consed system to compare to the staden system, and this is where I'd like some feedback. If I thought setting up staden was a little tedious, then setting up consed (with the phred/phrap support programs) is at least a couple of levels more difficult. I still don't know if it is worth the effort. The consed documentation states you should spend at least 6 hours reading the manual and testing the various functions! There are lots of files to alter, place in various directories, you have to choose options and handle specific naming systems for trace files.
My impression so far is that the consed editor is much more powerful than the gap4 editor of staden but I'm concerned that assembling sequence reads is not going to be as easy as gap4. The consed editing window is very nice, and bringing up chromatogram traces, individually or in alignment, is excellent. The number of options and ability to manage contigs is amazing. So is the learning curve!
Comments about Gap4 and Consed would be appreciated.
BTW, a much cheaper alternative to sequencher is being developed (http://dnabaser.com/home.html), initially for windows, but the developers also intend to release for linux/OS X. In addition, the vector NTI suite is available free for academic use (but I believe it currently only runs on 10.3.x).
Mike Dyall-Smith
Phred/Phrap/Consed on a Mac
This was a henious project, but it is doable. I have a decent knowledge of unix, the major problems are actually covered in the consed documentation. David Gordon wrote it to make it as easy as possible to understand, and he explains error messages and what to do about them. So does Phil Green in the phred/phrap documentation. It's worth the work. I only use this software, because of its major versitility. I can do almost anything with these programs. Fake reads, backbones, inserting known sequences to act as magnetic reads for your ab1 files. I love it. However, it does take a commitment to learning more about unix than you did before. You have to learn to change shells, to edit .cshrc files, to edit the phredPhrap script so that it contains the right mobility file definitions... changing the location of the executable shell command "nice" in the script since it's listed as being somewhere else. Lots of little things like this. But it's absolutely worth it. I wouldn't know how to put it on a server, it practically killed me to figure out how to put it on a G5 in the first place. I miss Xwin-32. Still, assembling sequence is easy as pie. Once phred and Phrap have created your .ace file, consed opens it up and you can do anything. You can add reads, tear them out, you can tear contigs in two, you can search for strings and allign your contigs in seconds and hit "join" and there you are. You can tell phrap not to overlap reads in a specific place if you keep getting misassemblies.
There is a learning curve, sure. But it's worth it. If you need help, email me at bethanyk@u.washington.edu. I got a lot of help from old friends making it work myself, the least I can do is offer the same help to others.
b
Thanks Bethanyk. I have been
Thanks Bethanyk. I have been using consed for a couple of weeks now and am really enjoying it. Your offer of help is appreciated. There are still things I havent' got quite right; for example I can't get the restriction digestion to work. It asks for a file that is not there, and I don't know how to generate it.
I note the discussion list for phrap is not well used, and the sign up instructions are rather inhibitory on postings. Could be a relationship there.
MDS