Add more parameter options for abyss-pe

Question

Add more parameter options for abyss-pe

Closed this issue 5 years ago · 4 comments

It would be nice for a user to have control over the parameter settings in abyss-pe, including the "p" option for minimum sequence identity.

Answer 1 · 2020-03-11T15:58:37.000Z

Aside from the -p option, which ones would be most useful to your work?

Answer 2 · 2020-03-13T15:10:46.000Z

Sorry for the late reply…this went to my junk mail for some reason. I think the -p option would be nice to try first. Julie and I are trying to figure out a way for aTRAM to assemble different alleles, which I think would require the user to change the consensus stringency in assembly software (i.e, can we force reads with 100% identity to assemble into contigs, vs. reads with e.g. 90% identity?). Based on the Abyss manual, I think the -p option is our best bet to get what we want, but I’m not sure. Thanks, Drew

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On Mar 11, 2020, at 11:58 AM, rafe ***@***.***> wrote: Aside from the -p option, which ones would be most useful to your work? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#279 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3QE7OVCEGDTS6MLZTGBTLRG6YMFANCNFSM4LDGCWUQ>.

Answer 3 · 2020-03-13T15:39:46.000Z

Because "p" is not a unique name for an argument, I called it "--abyss-p".

Answer 4 · 2020-03-13T15:42:03.000Z

Ok thanks.

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On Mar 13, 2020, at 11:40 AM, rafe ***@***.***> wrote: Because "p" is not a unique name for an argument, I called it "--abyss-p". — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#279 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3QE7PT67KYGXIPGFMHEU3RHJHVDANCNFSM4LDGCWUQ>.