Project description

The aim of this project is to build a "long read assembly analysis tool" that allows one to load an assembly of long reads in GFA format and then explore and analyze the assembly graph in different ways.

The program will provide different views of the assembly, the contigs that it contains and the topology of the graph.

The user will be able to import different "annotations" of the graph, for example, taxonomic assignments of different contigs. The program will allow the user to visualize the annotations in the context of the graph, or to sort order select contigs by annotation.

The program will produce different plots, such as bubble plots showing contig size as a function of GC-content and coverage.

The GUI and visualization will be implemented in Java 12 using OpenJFX. 

Prerequisites

• Java
• Basic bioinformatics
• This project is in English