General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Simple Assembly of Sanger Sequencing Files with MacVector Assembler

With MacVector Assembler, assembling ABI Sanger Sequencing files is simple, fast and accurate. MacVector uses the popular phred/phrap/cross_match set of tools from the University of Washington. To improve accuracy, and to help resolve repeats, these tools use “quality scores” (popularly known as “phred scores”), giving them an advantage over many other methods. To assemble two or more ABI files, follow these steps.

  • Use File | New | Assembly Project to create a new project
  • Click on the Add Seqs toolbar button and select all of your ABI (or SCF) chromatogram files to import
  • Click on the phred toolbar button – this re-calls the traces and generates quality scores (no need to select any items in the project, though you can to run phred on specific files)
  • Click on the phrap toolbar button and accept the defaults
  • After phrap has run, you will be presented with one or more contigs (assuming your ABI reads actually overlap). If you double-click on one of those, a contig editor will open letting you view and edit the actual alignments.

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    Not sure if you have Assembler? Choose MacVector | About MacVector. If the screen that appears says “MacVector with Assembler, Pro Edition” then you have it. If not, you can sign up for a fully functional 21 day trial version.

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