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Note the status area at the bottom with the text "Finished calling bases". Click on the triangle before the trash to expand it, which shows you this view: When the base calling step is complete, the progress dialog disappears, and the project window changes - you now see 7 samples in the "Unassembled Samples" folder, and 7 samples in the "Trash" folder. Typically, base calling takes only one or a few seconds per sample. imports the result files produced by PHRED the original files are renamed and moved to the trash.starts PHRED (which is a separate program), telling PHRED to call bases for all the files in this temporary directory.

exports the selected samples into a temporary directory.

You will see a progress dialog, while Aligner does the following steps:

Go to the " Sample" menu, and select " Call Bases" (if the menu item is greyed out, you have not selected one or more unassembled samples note that you cannot base call samples in contigs).

Typically, you would base call all samples in your "Unassembled Samples" folder - so just click on the "Unassembled Samples" folder to select it.

In the project view, select the samples that you want to base call.

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If you are using Aligner in demo mode, and your sequences do not have quality scores or you want to try the base calling, please request a trial license before proceeding.

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To do the "Base Calling" step in Aligner, you will need a trial license or a purchased full license. If the numbers are not 0, the samples have quality scores (make sure that you see the actual samples, not just the folder they are in - the quality scores for folders are always 0). For samples that you not have quality scores, the number in the "Quality" column is 0 for all samples. Tip: If you are not sure if your sequences have quality scores, look at the "Quality" column in the project view for your samples. If your sequences already have quality scores (for example because they were processed by the "KB" base caller from ABI, you can skip this step and go on to end clipping. You should do this step if you have sequence traces without quality scores. Aligner allows you to run PHRED on Aligner projects in a single step. PHRED was developed and copyrighted by Phil Green and co-workers at the University of Washington, and is often viewed as the "Gold Standard" for base calling. Base Calling withPHRED Why base call?ĬodonCode Aligner works best if your data have base-specific quality scores, like those assigned by the base calling program PHRED. Depending on the nature of your data, however, you may get better and "cleaner" assemblies if you do all the preprocessing steps in the order shown above. Note that the first three steps are optional - you do not have to do any of the first three steps before assembly.

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This section of the quick tour shows you how to process samples before an assembly, and how to assemble contigs.

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To apply for a free CodonCode Aligner license, please follow the license grant application instructions.Quick Tour: From Base Calling to Assembly From Base Calling to Assembly The Free License Grant Program was announced in a press release on May 6, 2009. CodonCode Corporation will make free personal licenses available on a regular basis to qualifying applicants (subject to the receipt of qualifying applications). Researchers at universities and non-profit organizations who would like to use CodonCode Aligner in their research, but do not have the funds to purchase a license, can apply for a free license.

If you would like to use CodonCode Aligner for more than 30 days in classes, or if your or your students may have used trial versions of CodonCode Aligner previously, please look at the detailed instructions for applying for teaching licenses. For short-term use (up to 30 days) in classes, the trial version of CodonCode Aligner may be sufficient, since every student who uses CodonCode Aligner for the first time will automatically get a fully functional 30-day trial after installing CodonCode Aligner.

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Teaching LicensesĮducators who want to use CodonCode Aligner in for college-level course work can apply for free temporary teaching licenses. CodonCode Corporation supports teaching and research by making free licenses available through two separate programs: teaching licenses and free license grants.