How to assemble using the batch mode. Tutorial: Assemble contigs from chromatogram (sequence) files using the batch mode. How to use DNA Baser Sequence Assembler

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?

Example1:

Let's say we have two samples that belong to the same contig:

Sequence A.scf
Sequence B.scf

The name pattern that we see is formed from:

an invariable part that is identical for both sequences ('Sequence ') and
a variable part that is unique for each sequence (in our case 'A' and 'B').

Therefore, we set the "Length of fixed part" to 9 because the fixed part had 9 characters (8 plus one space):

Example2:

In the screenshot below we have two input samples:

E10B016TF.scf
E10B016TR.scf

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.

TUTORIAL

Assemble thousands of samples in minutes!

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. 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).

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):

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 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 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.