[MUMmer-help] NUCmer - show-tilling

[DESPLAT, N. <Nel...@bi...>]

Hello,
I have a draft genome with multiple scaffolds (≈800 Mb) and a reference genome (2.5Gb).
I want to determine the position and orientation of these scaffolds in relation to my reference genome using nucmer (MUMmer3.22).
Here are my command lines, according to the documentation page here (http://mummer.sourceforge.net/examples/#nucmer) :
nucmer -p output -mum reference.fasta scaffold.fasta
delta-filter -i 90 -u 0 -q -r -l 100 output.delta > output.filter
show-coords -rcl output.filter > output.filter.coords
show-tiling -v 50 -g -1 -p output.fasta output.filter > output.tiling
For show-tilling, I used -p option to create a pseudo molecule with the scaffolds.
I would like understand how this programm creates the pseudo molecules because I have observed strange things.
For example, show-tilling give me this output file :
> Chr1
...
4927886          4941005          35706  13120  87.17   99.70   +         scaffold_27425
4976712          4989443          -5294   12732  73.63   97.01   +         scaffold_28410
4984150          5029997          4990    45848  93.02   98.31   +         scaffold_2130
5034988          5036622          8513    1635    100.00 99.88   +         scaffold_63004
5045136          5052379          -1891   7244    97.87   96.75   -           scaffold_44222
...
But when I look at the sequence at these positions in the fasta file, I can see that some scaffolds are missing (scaffold_2130) or truncated (scaffold_27425). The scaffold_2130 seems to be replaced by a gap of the size of the two gaps around this scaffold (4990 + 8513).
Can you please tell me how the scaffolds are used to create the chromosome based on the information of the tilling file?
Thanks for your help.

Nelly Desplat

Bioinformatics Engineer
Upstream Genomics

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