Introduction to Contiguity
- Introduction to Contiguity =============================
Contiguity is a Python application that allows the interactive visualization and manipulation of unfinished de novo genome assemblies, chiefly bacterial genomes. It enables a user to create and display information about contig adjacency via a graphical user interface (GUI). Sequence comparisons between the assembled contigs and a reference sequence can be displayed simultaneously to help guide the resolution of novel sequence or structural variants in a draft assembly. Contiguity also provides the first sequencing and assembly independent approach for the creation of contig adjacency graphs. Read pair mapping, sequence overlap and De Bruijn graph exploration are combined to maximize the number of adjacencies found during graph construction. By combining adjacency information with comparative genomics, Contiguity provides an intuitive approach for exploring and improving sequence assemblies. It is also ideally suited for guiding manual closure of Pacific Biosciences SMRT sequence assemblies of bacterial genomes. Contiguity is an open source application, implemented using Python and the Tkinter GUI package that can run on any Unix, OSX and Windows operating system.
Comparison of an Illmuina assembly of E. coli to a virulence plasmid visualised with Contiguity.
The Plasmid reference is shown in green. BLAST hits and inverted BLAST hits are shown in blue and orange respectively. Contigs are displayed in purple, a shortened version of the contig name on the contig when room allows. Its orientation and length is also shown where possible. If read information suggests that these contigs may be adjacent to each other, they are joined by a curved black line. This plasmid has been misassembled by Velvet (tsk tsk).