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Update to use Nextflow pipelines bacQC-ONT and assembleBAC-ONT #15

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Tracked by #14
tavareshugo opened this issue Nov 20, 2023 · 2 comments
Open
Tracked by #14

Update to use Nextflow pipelines bacQC-ONT and assembleBAC-ONT #15

tavareshugo opened this issue Nov 20, 2023 · 2 comments
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@avantonder

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@tavareshugo
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Need to change the assembly section to use this instead:

https://github.com/avantonder/assembleBAC-ONT
@tavareshugo
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Test the pipeline and see if the outputs are all there for the exercises

@tavareshugo tavareshugo changed the title Update pipeline to use avantonder/assembleBAC-ONT Update to use Nextflow pipelines bacQC-ONT and assembleBAC-ONT Dec 21, 2023
@tavareshugo tavareshugo mentioned this issue Dec 21, 2023
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@tavareshugo
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Updates needed:

  • section 6 preparing data should use samplesheet
  • section 7 read content should use bacQC-ONT
  • section 8 assembly should use assembleBAC-ONT
  • section 9 assembly quality revise to match output of assembleBAC
  • section 11 MLST revise to match output of assembleBAC
  • update slides corresponding to all those sections
  • (optional) Microreact instead of FigTree

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@tavareshugo @avantonder