I have done genome assembly on a bacteria sample using SPAdes and Velvet. I have a contigs file from each of the assemblers. How can I compare these two files to see if their results are different or not?
I ended up using progressiveMauve, MUMmer (specifically MUMmerplots), QUAST, and clc_sequence_info (from CLC Genomics Workbench) altogether and I could come to some conclusions based on the results of all these methods.
Check this thread - it is old, but answers kept being added. In addition to QUAST, see BUSCO (checks for conserved gene content) and something like ALE or REAPR (assembly quality based on mapping metrics).