Sequencer software

By genehckr at Sun, Sep 18 2005 2:12am |

Can anyone reccomend a good DNA sequence data file viewer/editor for OS X? Thanks.

‹ staden gap4 versus phrap/consed (instead of sequencher) optimising C/C++ code on G5s etc ›

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Tue, 2005-09-27 00:11 — cparnot

4Peaks

check out mekentosj.com

Tue, 2005-09-27 00:18 — biotrix

4Peaks is awesome!

Where has this app been all of my life. This is one of the most polished bioinformatics apps I've seen on OS X.

Sat, 2006-01-07 09:02 — tallers

MacVector

If you can afford it, MacVector is great. But it is expensive.
http://www.accelrys.com/products/macvector/

Thu, 2006-03-30 13:50 — Roger

yes!

I've been using 4peaks for almost one year and it's great... the guys at mekentosj.com also have some other good stuff, that worth to check out

Wed, 2006-05-10 20:42 — bethanyk

Sequencer Software

I hate to throw a wrench in the works, but I use phred/Phrap/consed. Even though it was a royal pain to get it to work on my G5, since I'm used to having my own sysadmin to do this kind of thing for me, it was worth it. You need to know some unix, pretty basic stuff like creating directory structure. You need to be able to use a text editor so you can add a few lines to the script and you need to know how to move files around so they are in the places they are expected to be in. But for doing serious assembly of chromat files, I would not use anything else. Ever. It looks threatening, because it is a unix-based program. But you can run X11 on your mac, switch your shell to csh and you're good to go. You only have to make sure that your files are in the right places, the specifics of the rest of it is really well covered in the documentation. In fact, while the docs are long, they cover everything, including the error messages you might get and how to fix them. Best of all it's free if you're accademic or non-profit. I can't recommend this high enough.

Thu, 2006-05-11 16:22 — Mike Dyall-Smith (not verified)

Sequencer Software

A few months ago I set up the STADEN package, with PHRAP (I couldn't get it to work properly without phrap). The mac installer for STADEN makes most of it very easy (double-click the installer and you are almost there). However, the PHRAP program you have to ask for (free for academic use) and that was the most hassle (unix-wise). The instructions are very good, even for unix novices, so that went OK. Using staden programs pregap (+phrap) to process .abi files, then gap4 to assemble and edit was a breeze for small numbers of trace files. I have not pushed it further as I then discovered CONSED, and I now use that. My experience is that staden is quicker to setup and use for small projects while consed is slower to setup, but has more features [am I wrong here?]. For example, in consed you have to set up a directory system for each project, consisting of at least 3 directories, etc. Staden requires none of this.
I would agree with Bethanyk that consed is very powerful, can handle any number of trace files, and gives you lots of flexibility in assembling and editing contigs. I only wish the idea of drag and drop would exist in the land of unix geekware. There is no easy way to install the package (eg using FINK), probably because the components are under strict licencing agreements and must be requested from separate developers.
The above comments are some of my impressions with both packages. I have learned a bit of unix, just enough to get by. This has been well worthwhile, for these packages are free, extremely powerful, and can be run on any mac running OS X. Compare this to the standard lab cost of a single licence for sequencher. For non-unix people who cannot stand the idea of Terminal.app or X11, there is a new program out that I believe will change the entire market (sequencher is the reason I now use consed). It is windows only at present, but is promised to become *nix flavoured. It is called Baser (google search it).
MDS.