For this walkthrough we will be comparing an E. coli genome with five other E. coli and mapping the read coverage from the underlying genome assembly onto the same image. Users will need BRIG-Example.zip, which is available from the BRIG website: https://sourceforge.net/projects/brig/files/. This contains all the genomes and files needed to follow along with this walk through. Unzip it somewhere easily accessible, like the home directory or desktop.
The walk through will work out of the unzipped BRIG-Example.zip folder. The walk through and related figures will use C:\BRIGEXAMPLE as that location.
Step 1: Load in sequences
To keep the final image consistent with the walk through, please open “ExampleProfile.xml” from the unzipped BRIG-Example.zip folder. This file configures BRIG to the same image settings in the walk through.
- First, set BRIGExample.fna as the reference sequence.
- Set unzipped BRIG-Example folder\genomes as the query sequence folder.
- Press “add to query pool”, this should load several items into the pool list.
- Set the unzipped BRIG-Example folder as the folder.
- The BLAST options box should be left blank.
- Click next
N.B: You can add individual files to your data pool too
Step 2: Configure rings
The next step is to configure what information is shown on each of the concentric rings in BRIG. Create six rings, for each ring:
- Set the legend text for each ring
- Select the required sequences from the data pool and click on “add data” to add to the ring list.
- Choose a colour
- Set the upper (90) and lower (70) identity threshold.
- Click on “add new ring” and repeat steps for each new ring required.
- Rings can be reordered by dragging them in the Ring List pane.
- You can set default threshold values in “BRIG options”.
- When using a Genbank/EMBL file as a reference, users can choose whether to use the protein or nucleotide sequence.
Configure each of the rings as the following:
- Ring 1:
- Legend text: GC Content
- Required sequences: GC Content
- Ring 2:
- Legend text: GC Skew
- Required sequences: GC Skew
- Ring 3:
- Legend text: Coverage
- Required seqeuences: BRIGExample.graph
- Colour: rgb value 153,0,0
- Ring 4:
- Legend text: O157:H7
- Required seqeunce: E_coli_O157H7Sakai.gbk
- Colour: rgb value 0,0,153
- Ring 5:
- Legend text: HS and K12
- Required sequence: E_coli_HS.fna, E_coli_K12MG1655.fna
- Colour rgb value 0,153,0
- Ring 6:
- Legend text: CFT073 and UTI89
- Required seqeunces: E_coli_CFT073.fna, E_coli_UTI89.fna
- Colour: rgb value 153,0,153
Step 3: Review and submit
The last window allows us to change the BLAST options, the location of the image file
and set the image title, which will appear in the centre of the ring. For the walkthrough configure the third window as
- Set the image title as “BRIG example image”.
- Hit submit.
- The image will be created in the specified output directory and should look something like the image below.
BRIG will format Genbank files, run BLAST, parse the results and render the image.
The final image below shows GC Content and Skew, the Genome coverage,
contig boundaries, and the BLAST results against the other E. coli genomes. The results for HS and
K12 have been collated into a single ring, likewise for UTI89 and CFT073.
N.B Image settings, like size, fonts, etc can be configured in: Main window > Preferences > Image options…