[MUMmer-help] Assessing draft assembly

[Rajiv M. <rm...@st...>]

Hi,

I am wondering about the most appropriate way to perform alignment 
between a draft genome assembly and a Drosophila reference genome 
sequence that could be used to estimate the proportion of the genome 
covered by the draft and compare different assemblies.

I took a look at the instructions here: 
http://mummer.sourceforge.net/manual/#mappingdraft, as well as some of 
the posts to this list, and it seemed like the "delta-filter -q" 
approach was preferred.  Does this ensure that each contig may only 
align to one position in the reference so that coverage is not 
artificially inflated?

Also, in some cases, my show-coords results show broken alignments to 
the same general region, presumably due to indels or assembly error, but 
sometimes the [COV Q] field adds up to more than 100%:

  2608802  2613586  |        1     4785  |     4785     4785  | 100.00  
| 23011544   170323  |     0.02     2.81  | 2L ctg100001147002
  2613579  2661256  |     8504    56174  |    47678 47671  | 99.99  | 
23011544   170323  |     0.21    27.99  | 2L ctg100001147002
  2663031  2752834  |    56164   145937  |    89804 89774  | 99.97  | 
23011544   170323  |     0.39    52.71  | 2L ctg100001147002
  2732783  2777220  |   125915   170323  |    44438 44409  | 99.93  | 
23011544   170323  |     0.19    26.07  | 2L ctg100001147002

Would this mean that some portion of the contig is aligning to multiple 
locations?

Thanks for your help!

Rajiv