Re: [MUMmer-help] Assessing draft assembly

[Adam P. <aph...@gm...>]

Hi Rajiv,
Please refer to the methods we used in the GAGE paper:

http://genome.cshlp.org/content/22/3/557.short

The supplemental materials for that paper include some basic scripts for
using Nucmer to assess assembly quality/completeness vs. a reference.

Best,
-Adam



On Wed, Mar 19, 2014 at 2:16 PM, Rajiv McCoy <rm...@st...> wrote:

> 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
>
>
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