Start CodonCode Aligner. If you just installed Aligner, you should see the startup dialog:
Click on "Open an existing project...", then press the OK button. (If you do not see the startup dialog, select "Open Project..." from the "File" menu).
This will show a standard "Open" dialog:
Navigate to the folder where you installed Aligner (the folder is called "CodonCode Aligner", and is in the "Applications" folder on OS X, and in the "Program Files" folder on Windows, unless you chose a different location). Then, go to the "Example Files" folder, and from there to the "Example1" folder. Select the "Example1.proj" file, and click "OK" (note that you may not see the ".proj" extension on Windows, depending on your settings).
Aligner will read the project information, which should take just a few seconds, and then open the "Project View" window:
The project contains 7 sequences, which are in the "Unassembled Samples" folder. Click on the triangle before the folder to see its contents:
You can click on the column headers to sort the sequences. The little triangle indicates which column is used for sorting, and in which order. In the picture above, samples are sorted by name (note that the Unassembled Samples folder will always be at the top, and the Trash at the bottom). Click on the "Length" header twice to sort by length in descending order. The project view should now lool like this:
The "Quality" column is worth a brief explanation. As a measure of the quality of each sample, it shows the number of bases with a quality score of at least 20 (often called "high quality" or "Phred20" bases). In the example above, all the values are close to each other; for "real world" data, the numbers can vary considerable. The quality column can make it easy to identy low-quality sequences. During the "end clipping" step, you can choose to have sequences with too few Phred20 bases moved to the trash automatically (as described on the following pages).
Within the project view, you can move samples from one folder to another by drag and drop. Try it out:
You can do this with any selection; if you select a the "Unassembled Samples" folder, then all samples in it will be moved. Try it out!
When you are done playing around, drag the samples from the trash back into the "Unassembled Samples" folder.
What you select in the contig view determines which menu items are available. In the picture above, the "Unassembled Samples" folder is selected. Therefore, menu items for samples, like "Call Bases..." and "Clip Ends..." in the "Sample" menu, and "Assemble" in the "Contig" menu, are enabled. Other menu items are disabled, like "Unassemble" in the "Contig" menu, which requires that a contig is selected.
The next section explains how to assemble contigs, and which steps you may want to do before assembly.
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