Level: beginner

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
• reverse-complemente of input files (if necessary)
• contig error correction
• vector removal using primer sequences (if option is checked)Let's start:

Building the project

Step 1.

Open DNA Baser by clicking its icon on your desktop. When DNA Baser starts, the Project Manager should open by default.

Navigate to the folder where your sample files are.

Step 2. (optional)

Open the Assembly Settings tab to choose the parameters for:

• Assembler engine
• Trimming engine (for trimming the untrusted regions of the chromatograms)
• Sequencing error correction

Note: In DNA Baser v2, these settings can be found in Settings window.

Step 3. (optional)

Select the primers you want to use for the removal of contaminant vector sequences.

Step 4. (optional)

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:

Step 5.

Select the samples that are going to be assembled by adding them to the Job List. Different file types (SCF, ABI, FASTA, SEQ, etc) can be mixed (assembled) together.

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

• use the button to add selected file/files to the Job List.
• use the button to add all files to the Job List.
• use the mouse to drag and drop files Sample Explorer to the Job List.

If you want to remove files from the Job List, use the button or press the Delete key.

Running the project

Step 6.

To start the assembly process, press the START button. During assembly, DNA Baser will:

• automatically detect and trim low quality regions of your samples
• automatically trim vector sequences
• automatically correct the ambiguities in your contig
• automatically save the project and the contig to disk

The program will show an explicit warning if you try to assemble less than two files. This can happen because DNA Baser removed some samples from the job because:

• one or more files in the Job List are invalid
• one or more files in the Job List have been removed from your computer's hard drive meanwhile.

Analyzing the results

Step 7.

After the assembly process, you should check the log window to see if there were any warnings/errors (invalid input files, unassembled files, etc) and to see the summary of the job (quality of the input files, total number of mismatches, metadata integration, etc). The errors are shown in red color; warnings in orange.

Step 8.

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

The next tutorial explains how to:

• edit the input samples
• correct the ambiguities
• remove vectors
• save the assembled contig.

If you have any questions, don't hesitate to contact us.