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SEQUENCE ASSEMBLY

Preparation

 

 

 

 

 

 

 

The process described below may seem lengthy. However, usually, you need to perform it rarely or only once (first time when you use DNA Baser). Once you set these settings they will be remembered, so next time you can proceed directly to sequence assembly process.

 

 

1. Select the assembly parameters (optional)

 

Most of the times, the default parameters for the Assembler Engine and Trimming Engine perform very well. Modify the parameters ONLY if you have samples that does not assemble.

 

 

2. Select recognition sequences for vector removal (optional)

 

When the sequencing is performed using primers from the vector, the resulted sequences will also contain parts belonging to the vector. These contaminating vector regions have to be removed from the final contig. DNA Baser is doing this automatically, at the end of the assembly process, when saving the contig. To identify the vector sequences, DNA Baser is using so called recognition sequences. Such vector recognition sequences are input by the user and they are specific the vector used or gene sequenced. For more details about the vector removal algorithm and how to create a database with vector recognition sequences, click here.

 

 

3. Select a reference (optional)

 

In the Assemble to reference panel you can specify that you want to assemble your samples to a reference sequence.

 

 

5. Other settings (optional)

 

In Project Options you can set DNA Baser to either move or copy the samples that cannot be assembled, in separate folders.

 

 

6. Proceed to sequence assembly

 

 

 

DNA assembly contig assembly

 

 

DNA trace assembly
DNA contig assembly
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