Comparing contigs results from two different assembler

Question

[']

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?

[poisonAlien]

Mummer maybe ?

[User 59]

Crossposted: http://seqanswers.com/forums/showthread.php?t=66042

Answer 1

[']

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.

[Medhat]

Great and what is the conclusions?

[GenoMax]

Perhaps the conclusions are only useful to @Lazarus. It appears to have taken 9 months to get to them :)

Answer 2

[aleimba]

There are several assembly metrics packages out there, if that's what you want. The most popular is QUAST (Quality Assessment Tool for Genome Assemblies):

http://bioinf.spbau.ru/quast

Answer 3

[h.mon]

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).