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Switch from HIVSeqinR to HIVIntact #10

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donkirkby opened this issue Jul 23, 2021 · 1 comment
Open

Switch from HIVSeqinR to HIVIntact #10

donkirkby opened this issue Jul 23, 2021 · 1 comment
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@Donaim

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@donkirkby
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donkirkby commented Jul 23, 2021 •
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Try using HIVIntact to determine which samples are intact.

HIVIntact is apparently designed for improved integration into analysis pipelines, and is more “customizable” than current tools (such as SeqinR).

One additional possible advantage of this program is that it appears to be able to handle HIV sequences belonging to different subtypes (as opposed to SeqinR which may not be appropriate for use on many (all?) non-B subtypes.
donkirkby added a commit that referenced this issue Jul 24, 2021
@donkirkby
Add HIVIntact analysis, for #10.
548cea6
donkirkby added a commit that referenced this issue Jul 26, 2021
@donkirkby
Include sqlite in Singularity, for #10.
d539b0a
donkirkby added a commit that referenced this issue Jul 26, 2021
@donkirkby
Make Pipfile compatible with GitHub Actions, for #10.
98bd8e3
donkirkby added a commit that referenced this issue Jul 26, 2021
@donkirkby
Install mafft in GitHub Actions, for #10.
7eabb28
@CBeelen CBeelen mentioned this issue Nov 30, 2022
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There's a paper related to the project.

@Donaim Donaim self-assigned this Jun 5, 2023
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Add HIVIntact analysis, for #10.
d7c2aae
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Install mafft and blast in GitHub Actions, for #10.
2ecdbbd
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Add HIVIntact analysis, for #10.
6dd4746
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Install mafft and blast in GitHub Actions, for #10.
ceda78c
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Add HIVIntact analysis, for #10.
f9f84f7
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Install mafft and blast in GitHub Actions, for #10.
ff574f7
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Add HIVIntact analysis, for #10.
55536fb
Donaim pushed a commit that referenced this issue Jul 21, 2023
@donkirkby @Donaim
Install mafft and blast in GitHub Actions, for #10.
1d54987
@Donaim Donaim mentioned this issue Jul 24, 2023
Merged
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