MUMmer plot full of dots and no diagonal lines

[dbob]

I know from the MUMmer manual that a perfect alignment should, ideally, show a red diagonal line going from the bottom to up in the plot. However, I used MUMmer plots to compare the results of the assemblies between Velvet and Minia (both assemblies performed using the same kmer size and same coverage cutoff). And I received the following plot, I am wondering whether this is good alignment or a terrible one?

[maubp]

If these are two related species, its a terrible alignment.

Which search algorithm did you use? It makes a big difference:

• mummer, efficiently locates maximal unique matches between two sequences
• NUCmer (NUCleotide MUMmer), for closely related sequences
• PROmer (PROtein MUMmer), using six frame translation of DNA input, for less similar sequences

[westerman]

You say "...results of the assemblies between Velvet and Minia ". How are the assemblies sorted? If they are not in the same order then the alignment will look random.

[maubp]

Actually back-tracking slightly, looking more closely at the vertical axis, all the contigs are so small that you won't see any diagonal lines in the mummer plot. The horizontal scale has some nice long contigs.

There is probably a mummer option to sort the contigs, in which case you'd hope to get dots on a diagonal...