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ENH: implement co-assembly option #22

Closed
2 tasks
misialq opened this issue Jun 27, 2022 · 1 comment · Fixed by #68
Closed
2 tasks

ENH: implement co-assembly option #22

misialq opened this issue Jun 27, 2022 · 1 comment · Fixed by #68
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@DorielaGrabocka
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enhancement New feature or request
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Manuscript prep

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@misialq
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misialq commented Jun 27, 2022 •
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As a plugin user,
I want to be able to co-assemble genomes across all the samples rather than per-sample
so that I can use all the available sequence information.

Tasks:

  • Implement co-assembly for MEGAHIT
  • Implement co-assembly for metaSPAdes

Depends on bokulich-lab/q2-types-genomics#77.
@misialq misialq added the enhancement New feature or request label Jun 27, 2022
@misialq misialq linked a pull request Jan 11, 2024 that will close this issue
ENH: co-assembling contigs from multiple samples (#22) #68
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@misialq misialq added this to the Manuscript prep milestone Jan 11, 2024
@misialq misialq mentioned this issue Jan 29, 2024
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@misialq misialq changed the title Implement co-assembly option ENH: implement co-assembly option Mar 14, 2024
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This PR/issue depends on: * bokulich-lab/q2-types-genomics#77

misialq added a commit that referenced this issue Mar 25, 2024
@DorielaGrabocka @misialq
ENH: co-assembling contigs from multiple samples (#22) (#68)
fd3ae4c 
* ENH: co-assembling contigs from multiple samples

* ENH: testing megahit co-assembling contigs from multiple samples done

* ENH: testing megahit co-assembling contigs 2 tests removed (for now)

* ENH: testing megahit co-assembling contigs 2 single-sample tests added

* ENH: testing megahit co-assembling contigs setup.py modified

* ENH: testing megahit co-assembling contigs 2 single-sample test files added

* ENH: testing megahit co-assembling contigs 2 single-sample single-end corrected

* ENH: testing megahit co-assembling contigs unused test functions removed

* ENH: coassembly in spades implemented

* ENH: coassembly in spades test implemented

* ENH: coassembly in spades test implemented path typo corrected

* ENH: coassembly changes requested done

* Use subprocess.run for file concatenation

* ENH: spades tests corrected

* ENH: FeatureData[Contig] added and working

---------

Co-authored-by: Michal Ziemski <mziemski@ethz.ch>
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ENH: co-assembling contigs from multiple samples (#22) DorielaGrabocka/q2-assembly
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@misialq @DorielaGrabocka