Batch sequence assembly based on subfolders|How to assemble using the batch mode. Assemble contigs from chromatogram (sequence) files using the batch mode

BATCH SEQUENCE ASSEMBLY

BY SUB-FOLDERS

Assemble thousands of samples in minutes!

Tutorial

Scenario

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. Placed in a separate folder

b. Named after a pattern (in this case see Batch sequence assembly by filename pattern)

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).

Fig.1 - The Project manager

Select the samples to be assembled

Navigate to the folder that contains your samples. Remember that samples that belong to the same contig need to be grouped in their own folders. You don't have to put these samples in the Job List. The sub-folder structure should look like this:

BATCH SEQUENCE ASSEMBLY BY SUB-FOLDERS - Folder struncture

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):

Output

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 based on the name of the folder in which the input files were located.

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

Unpaired

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