Assembly graphs

Assembled genomes (all the sequencing reads joined together) can be represented as a sequence in a FASTA file, but also as an assembly graph (edges and nodes, not usually linear).

• Overview of assembly graphs: https://github.com/rrwick/Unicycler#assembly-graphs
• De-bruijn graphs - video by Ben Langmead - https://www.youtube.com/watch?v=TNYZZKrjCSk
• Flye assembler - uses repeat graphs (slightly different): https://github.com/fenderglass/Flye#repeat-graph

How to view

• Bandage: https://rrwick.github.io/Bandage/
• AGB: https://almiheenko.github.io/AGB/manual.html
• GraphViz: https://graphviz.readthedocs.io/en/stable/manual.html