Assembly Graph inspection with bandage
Bandage is a program for visualising de novo assembly graphs. By displaying connections which are not present in the contigs file, Bandage opens up new possibilities for analysing de novo assemblies.
You can start Bandage with:
Bandage
and load the following file:
~/workdir/assembly/assembly_graph.gfa
and click on “Draw Graph” This is the assembly graph of our Nanopore Assembly. You can BLAST your contigs vs each other to identify further assembly problems by clicking “Create/View BLAST search”.
Compare this graph to a graph computed with Illumina data:
~/workdir/results/illumina_assembly/assembly_graph_with_scaffolds.gfa