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In order to assemble samples at batch, DNA Baser needs to detect which files should be assembled together. Therefore, your samples must be named in a recognizable pattern based on their membership to a contig. In Batch Assembly Parameters tab (see figure below), you can define the characteristics of your name pattern.




How to use it?


Example 1a:

Let's suppose we have a set consisting of two files:

  • EColli7F.SCF
  • EColli7R.SCF

The characters that are common (invariables) for both files are "EColli7", while the character that variates is "F" and "R".

Therefore, we use the mouse to select the invariable part: EColli7. Now the program will know that EColli7F and EColli7R belong to the same contig.




Example 1b:

Let's suppose we have two sets. Each set has two files:


  • CMO_272_K14.scf
  • CMO_272_M14.scf


  • CMO_272_K16.scf
  • CMO_272_M16.scf

We see that the first set has an invariable part: 14. The second set has also an invariable part: 16.
We use the mouse to select those two characters that are invariable (the program will show only the first sequence from your Job List):

batch dna sequence assembly by file name pattern



Example 2 (using separator):

Let''s suppose we have a set consisting of two files with variable name length:

  • 30_00A.ABI
  • 440_00A.ABI

The first part of the name does not follow a pattern so it is useless. However, the characters after the underscore ("00A") are common (invariables) for both files

Therefore, enter the underscore in the 'Separator' box and tell the program that 'The second part of the name is invariable'.

dna sequence assembly by file name pattern








Assemble thousands of samples in minutes!








You have a clone library of 500 sequences and you use two primers (Forward and Reverse) to sequence each clone. At the end of sequencing process, you will have a folder with 1000 sequences, which need to be assembled in 500 contigs. It would be rather tedious to assemble a contig at a time. However, DNA Baser is the only software that allows you to assemble all sequences in one-step. The prerequisite is that the sequences that belong to the same contig are:

a. Named after a pattern


b. Placed in a separate folder (in this case see Batch sequence assembly by sub-folders)




Let's start


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


DNA assembly contig assembly

Select the samples to be assembled


Add all samples that you want to assemble into the JOB LIST.



Set the name pattern


DNA Baser detects the pairs of samples based on the name of the sequences. Please visit this page to see how you should set the pattern.



Start the assembly


To start the assembly, just press the START BATCH 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.





Job complete!


During the batch assembly process, a detailed log is generated. It contains information about each individual assembling process, a batch job summary, the list of parameters used for assembling, quality of each assembly job and many many other statistics.


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



This is the folder were the new created contigs are saved. Each contig will be save in an individual FASTA or SEQ file. Each file is named with the prefix "contig" and a suffix indicating the invariable part of the original sample file. For example if the input files for a contig were E10B082TF.scf and E10B082TR.scf, the contig will be named "Contig - E10B081T".

For your commodity, DNA Sequence Assembler will also save all contigs together, in a single multiFasta file. Its file name derives from the name of the current folder.


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.


Samples that have no pairs will be moved/copied in this folder.





Related topics:



DNA trace assembly
DNA contig assembly
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