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LO - 3 - Alignments #28

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GavinHuttley opened this issue Oct 17, 2023 · 2 comments
Closed

LO - 3 - Alignments #28

GavinHuttley opened this issue Oct 17, 2023 · 2 comments
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@fredjaya @KatherineCaley
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block 3 learning outcome

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@GavinHuttley
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GavinHuttley commented Oct 17, 2023 •
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  • identifying divergent sequences prior to alignment and their relationships (using k-mer based tree estimation)
  • using cogent3 to align, the app, memory, speed, parameters
  • quantifying alignment quality using dotplots showing alignment path between most divergent sequences
  • information plots, plotting gaps
  • Alignment.count_gaps_per_seq(induced_by, unique)
  • Alignment.omit_bad_seqs()
@GavinHuttley GavinHuttley self-assigned this Oct 17, 2023
@KatherineCaley
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I have passed on some rough code to @fredjaya to document

@GavinHuttley GavinHuttley changed the title LO - Alignments LO - 3 - Alignments Nov 12, 2023
This was referenced Nov 12, 2023
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@KatherineCaley
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Closing as contented related to this issue will be described in #40

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@GavinHuttley @fredjaya @KatherineCaley