BATCH SEQUENCE ASSEMBLY
BY NAME PATTERN
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.
Based on the invariable part (see the figure above), the software will recognize that two (or more) samples belong to the same contig. The file extension is shown in gray color because it is irrelevant (we ignore it). The length of the invariable and variable parts must be the same for all sequences.
How to use it?
Let's say we have two samples that belong to the same contig:
The name pattern that we see is formed from:
Therefore, we set the "Length of fixed part" to 9 because the fixed part had 9 characters (8 plus one space):
In the screenshot below we have two input samples:
We see that the invariable part is E10B016T (8 characters long) and the part that changes is T and F respectively. Therefore we set the "Length of fixed part" to 8.
Assemble thousands of samples in minutes!
You have a clone library with 500 clones 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)
Select the samples to be assembled
Set the name 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.
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):
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