Assembly Visualiser using Java

Java program for visualising assembly scaffolds or contigs and compute the assembly quality metrics N50, Average scaffold/contig length, Total length, Largest scaffold and largest contig, total no. of contigs.

Requirements

• This program requires Java vesrion 8 or later installed.
• The program uses jfreechart-1.0.23.jar and jcommon-1.0.19.jar to compute and display the bar chart. These two files are attached within this repository. You will need to add them to libraries if it is being run using an IDE.
• The datasets genome.scf.fasta and Blast2GO_gff.gff are available within this repository.

The distribution Assembly_Viewer.jar file is found in the Assembly_Visualiser/dist folder. Running this .jar file will open up the GUI window where user can load both FASTA and GFF files using the file menu.

Note: Larger assemblies take longer to load. The genome.scf.fasta may take 20-30 seconds to load as it perform statisitcs and visualisation in the background.

Expected Results

In the image above:

• The "Assembly information" section shows the filename of the assembly along with its essential statistics like No.of sequences, N50, Average sequence length, Total length, and the largest sewuence length.
• The Text area below "Assembly information" section shows the sequence of the very first contig of the assembly.
• The labels below the sequence show "contig length", and the "GC content" of displayed/selected contig/scaffold.
• The scroll bar shows the identifier of the scaffold/contig that is displayed in the text area.
• User can select desired scaffold using the scroll bar to get the sequence, the contig length and the GC content of that contig.
• The program visualises the the contig/scaffolds in the "Bar Chart" area. It highlights the contig of N50 in blue color.
• The sequence ID, Type, Start & End positions, and the Scores are displayed in the table once the GFF file is loaded using "File" tab.