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How to use DNA Baser Assembler
Part 1


How to assemble two chromatogram files 

 


Level: beginner
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This tutorial will show you how to assemble contigs from chromatogram/fasta/seq files. During the assembly the following steps are automatically performed:

 

  - trimming of the low quality bases at the end of the chromatogram
  - assembling into a contig
  - error correction
  - vector removal using primer sequences (if option is checked)Let's start:

 

 

Starting the alignment process:

 

1. Open DNA Baser by clicking its icon on your desktop. When DNA Baser starts, the Project Manager should be opened by default. Navigate to the folder where your files are.


DNA assembly contig assembly

 

2. Open the Settings window and navigate to the Assembler engine tab. Here you can choose the parameters for assembling the contig, trimming the bad ends of the chromatograms and mismatch (sequencing error) correction.

 

DNA assembly settings

 

3. Select the primers you want to use for the removal of contaminant vector sequences. Click here to read how to do this.

 

4. Next step is to choose a name for this current project. DNA Baser will automatically choose a name for you but you can change it. Use this box to choose/change project's name: contig assembly name

 

5. Select two or more files that are going to be assembled by adding them to the JOB LIST. DNA Baser supports SCF, ABI, FASTA and SEQ.

You can add files to the Job List in several ways:

-use the sequence assembly software button to add selected file/files to the Job List.
-use the DNA trace assembly button to add all files to the Job List.
-using your mouse, drag and drop files one by one from File List to the Job List.
If you want to remove files from the Job List, than use chromatogram assembly button.
6. The final step is to press the START chromatogram assembly button. In this moment, DNA Baser should begin the assembling process.

dna assembly software If something is wrong, the START button will be disabled:sequence assembly software

 

This can be caused by:
   - less than 2 files in the Job List
   - invalid combinations of file types in the Job List
   - one or more files in the Job List are invalid or it has been removed from your computer's hard disk meanwhile.


7. After the assembly process, you can check the log window.

DNA assembly download


8. The assembled sequence, the corresponding chromatograms and the consensus contig are displayed in the assembly window.

 

assembly window

 

Read the next Next chapter tutorial to find out how to edit, remove vectors and save the assembled contig. If you have any questions, don't hesitate to write an email to us or to use our forum for support.

 

Note: Different file types can be mixed together. For example you can assemble ABI, SCF and FASTA sequences together.

DNA trace assembly
DNA contig assembly