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Implement Gibson Assembly #359

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carreter opened this issue Sep 23, 2023 · 5 comments
Open

Implement Gibson Assembly #359

carreter opened this issue Sep 23, 2023 · 5 comments
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enhancement New feature or request high priority High priority - something is broken or missing that is critical for users or developers. intermediate Will take some time to fix
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@carreter
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carreter commented Sep 23, 2023

Blocked by #367

@carreter carreter added this to the v1.0 milestone Sep 23, 2023
@carreter carreter added the needs-triage An issue that needs to be triaged label Sep 23, 2023
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carreter commented Sep 23, 2023

@TimothyStiles can you elaborate on what exactly it is we need here and triage the issue here + in the roadmap?

@Koeng101
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I think I can explain a little bit.

Gibson Assembly is an extremely popular DNA assembly method. It's used by pretty much everyone who isn't doing high-throughput work (where GoldenGate usually works better, which we do have).

Fundamentally, pretty much all DNA assembly methods use some form of overlapping sticky DNA ends which are then ligated together. In restriction enzyme cloning, these overhangs are created with enzymes that cut the DNA. In Gibson, you take blunted fragments and chew back about 20bp-40bp, which is then used as the overlap region (an idea originally adapted from yeast, which do this naturally).

So, with just a few additions, we could probably adapt our clone library to do Gibson. However, I think the clone library out of all our packages (other than parsers) could really use a revamp. It's kinda convoluted right now, and I think it could be simplified by quite a bit.

Gibson assembly I think is important enough that we should have it on the roadmap.

@carreter carreter added enhancement New feature or request high priority High priority - something is broken or missing that is critical for users or developers. easy A quick and easy fix! and removed needs-triage An issue that needs to be triaged labels Sep 23, 2023
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github-actions bot commented Sep 23, 2023

Status: Ready to merge ✔️

Issues blocking this PR:


This comment was automatically written by the Blocking Issues bot, and this PR will be monitored for further progress.

@github-actions github-actions bot added the blocked Waiting for another PR/issue to be merged/closed. label Sep 23, 2023
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This issue has had no activity in the past 2 months. Marking as stale.

@github-actions github-actions bot added stale and removed blocked Waiting for another PR/issue to be merged/closed. labels Nov 23, 2023
@github-actions github-actions bot removed the stale label Nov 30, 2023
@carreter carreter self-assigned this Dec 20, 2023
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This issue has had no activity in the past 2 months. Marking as stale.

@github-actions github-actions bot added the stale label Feb 18, 2024
@carreter carreter added intermediate Will take some time to fix and removed easy A quick and easy fix! labels Sep 10, 2024
@github-actions github-actions bot removed the stale label Sep 10, 2024
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