DNA Sequence Assembler. Single contig assembly|Assemble sequence (chromatogram) files. DNA BASER-automatic DNA sequence assembly, vector removal, metadata integration, contig editing

Standard sequence assembly

with DNA Baser

Introduction

Use the SINGLE CONTIG ASSEMBLY function to assemble two or more samples into a contig. DNA Baser supports all popular formats: SCF, ABI, FASTA, SEQ, TXT, SEQ. It is possible to assemble samples of different types, for example SCF and FASTA files, or ABI and SEQ files.

Hint: We strongly recommend you to use DNA chromatograms files (SCF/ABI) instead of FASTA files, because they contain information on the confidence scores (confidence score) of the bases. This enables DNA Baser to automatically correct the ambiguities with a very high precision.

While with other tools the user needs to manually perform basically every single step of the assembly, with DNA Baser the following steps are automated:

Starting the sequence assembly process

1. Preparation

Start DNA Baser. The Project Manager should open by default. Prepare DNA Baser for sequence assembly (you need to perform this step only once).

2. Output settings

In the 'Project Name' panel (see Fig 1) you can set the path where DNA Baser will write the output (contigs, project, log, etc) and the name under which the output will be saved.

Important! You don't have to manually set any of the above parameters. The program detects and sets the best values for you.

3. Select the samples to be assembled

Add all samples that you want to assemble into the JOB LIST. If necessary also add a reference squence.

5. Start the assembly

To start the assembly, just press the START CONTIG ASSEMBLY button. DNA Baser will detect the samples belonging to the same contig and assemble them. Don't leave the computer. DNA Baser will finish before you have the time to drink your coffee.

Figure 1.

Job complete!

During the assembly process a detailed log is generated. It contains information about the contig, the list of parameters used for assembling, quality of the assembly and many many other statistics. The assembled sequences, the corresponding chromatograms, the consensus contig and the contig map are displayed in the ASSEMBLY WINDOW (see figure below). The user can use the AMBIGUITY NAVIGATION SYSTEM to rapidly check the contig. When done, pressing on the FINISH button will save the contig.

During assembly, DNA Baser may creates the following folders (located in current folder):

Unassembled

Samples that cannot be assembled to contigs will be moved/copied (depending on user settings defined in Project Options) in this folder. You may want to relax the assembling parameters and try again to assemble the files in this folder.