I'm trying to ascertain whether PBJelly (current version) incorporates the scaffolding function suggested in the discussion of English et al. 2012: does it link contigs together by the long pacBio reads to generate a better-scaffolded assembly?
My assembly currently has almost no gaps, but does need better scaffolding. If PBJelly isn't able to do this--do you know of software that can perform this function?
Thanks in advance,
John
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The current version of PBJelly does attempt super-scaffolding and with long enough read lengths, will join scaffold ends. However, we do not have contig/scaffold incorporation into gaps. (e.g. scaffold A has a gap and contig B belongs inside of it.)
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Hi,
I'm trying to ascertain whether PBJelly (current version) incorporates the scaffolding function suggested in the discussion of English et al. 2012: does it link contigs together by the long pacBio reads to generate a better-scaffolded assembly?
My assembly currently has almost no gaps, but does need better scaffolding. If PBJelly isn't able to do this--do you know of software that can perform this function?
Thanks in advance,
John
The current version of PBJelly does attempt super-scaffolding and with long enough read lengths, will join scaffold ends. However, we do not have contig/scaffold incorporation into gaps. (e.g. scaffold A has a gap and contig B belongs inside of it.)
Thanks Adam, this should be perfect for what we are doing.
Best,
John