abyss-sealer

[Matthew MacManes]

Hi All, 

I see abyss-sealer is included in abyss-pe, but not sure how to call it- does not seem to be run by default. Any tips about getting this up and running as part of the abyss-pe pipeline?

[Matthew MacManes]

ok, I just edited the abyss-pe makefile and submitted a pull request. Not sure if the functionality was non included intentionally or not.

[Ben Vandervalk]

Hi Matt,

abyss-sealer is disabled by default because it sometimes has unpredictably long run times at low k values.  See for example: https://github.com/bcgsc/abyss/issues/79

That said, the tool is highly useful and generally produces good results, but sometimes you have to fiddle with the parameters to get reasonable execution times.

When we sort the run time issue out, we will make it part of the pipeline by default.

- Ben

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[Matthew MacManes]

Thanks Ben. So is there are way to run sealer from abyss-pe **without** having to edit the makefile?

Matt

[Ben Vandervalk]

Hi Matt,

I think if you explicitly append the target $name-8_scaffold.fa to your abyss-pe command line, it will do the normal assembly pipeline and then run Sealer afterwards for a range k values, i.e.

$ abyss-pe name=foo <..your_usual_abyss_pe_args> foo-8_scaffold.fa

where the final (sealed) output file is foo-8_scaffold.fa.

You can test it by adding the --dry-run (-n) option at the end, to see what commands would be run without actually them.

- Ben