[MUMmer-help] dnadiff very slow for Human

[Davide V. (GIS) <ver...@gi...>]

Dear MUMmer users,

We are trying to apply dnadiff for the analysis of breakpoints between our de novo Human genome assembly and the Reference genome, the latter divided into multiple chromosomes / separate files.

We have already computed a NUCmer comparison between the two assemblies and the related delta file.  After this, we tried to compare all our scaffolds versus hg19 chromosome 1 using dnadiff, and the tool lasted more than 12 days (1 single core used, peak of 24 Gb RAM) before crashing (for internal server reasons), without writing any temporary file (apart from the log line "Filtering alignments") and presumably just trying to run "delta-filter -1".  Did you already face this problem?  Is there a way or script to speed up dnadiff for the Human genome comparison?

Thanks and regards,
Davide

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