Any recommended gap-closer?

[andreaswallberg]

Dear developers,

I wonder if you have any software recommendations or other considerations for running gap-closing after scaffolding with ScaffMatch?

Which tools would you recommend for gap-closing with long-reads, for instance?

Are gap lengths proportional to estimated gaps or mostly arbitrary?

[mandricigor]

Dear Andreas, We recommend using Gap2Seq with ScaffMatch: https://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq/. Gap lengths produced by ScaffMatch should be in a sense proportional to the real gap lengths. Thanks for using ScaffMatch, Igor пн, 31 авг. 2020 г. в 14:20, Andreas Wallberg <notifications@github.com>:

…

Dear developers, I wonder if you have any software recommendations or other considerations for running gap-closing after scaffolding with ScaffMatch? Which tools would you recommend for gap-closing with long-reads, for instance? Are gap lengths proportional to estimated gaps or mostly arbitrary? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABKOWCV4WPF4TYO5LYLOAYTSDQHYPANCNFSM4QQ6OOHQ> .