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Commits on Jan 5, 2024

• first draft bas manuscript for internal rev

  jtsumner

  committed
  36a9008

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Commits on Nov 6, 2023

• updated to fix read pair naming

  jtsumner

  committed
  e8d6263

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Commits on Nov 2, 2023

• parameter adjustments and prepping to tweak mpa and humann

  jtsumner

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  f2d3cc6

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Commits on Oct 10, 2023

• humann regrouped added

  jtsumner

  committed
  778ce05

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• updated assembly resources and humann regrouping

  jtsumner

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  8880234

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Commits on Oct 6, 2023

• manuscript update

  jtsumner

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  0347051

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Commits on Sep 1, 2023

• R integrated for visuals beta

  jtsumner

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  2523e4d

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Commits on Aug 26, 2023

• humann cpm norm added

  jtsumner

  committed
  a3e69f0

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Commits on Aug 24, 2023

• merged bracken and humann norm beta added

  jtsumner

  committed
  51cc920

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• bracken and kraken2 new database

  jtsumner

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  433f7df

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Commits on Aug 23, 2023

• humann and mpa merged added to config

  jtsumner

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  20787c2

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• merged humann and high kmer spades

  jtsumner

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  dd43dca

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Commits on Aug 14, 2023

• added humann and small updates to bowtie very-sensitive and log location

  jtsumner

  committed
  e1e1d63

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Commits on Aug 8, 2023

• updated eggnog

  jtsumner

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  b333532

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Commits on Jul 20, 2023

• added eggnog mapper

  jtsumner

  committed
  afa17c1

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Commits on Jul 19, 2023

• beta add prokka checkm and viral to rule all solver

  jtsumner

  committed
  3a648e2

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• host decontamination implemented in rule solver

  jtsumner

  committed
  16a3bf5

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• negative control-contaminants removal added

  jtsumner

  committed
  03de11a

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Commits on Jul 17, 2023

• prokka after assembly

  jtsumner

  committed
  3ac3d77

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Commits on Jul 14, 2023

• reorganized files

  jtsumner

  committed
  221e5c6

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Commits on Jul 13, 2023

• parse contigs works

  jtsumner

  committed
  df6e766

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• mpa4 and others

  jtsumner

  committed
  37228a0

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Commits on Jun 22, 2023

• huge update: viral, binning, visualization

  jtsumner

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  520f6b4

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Commits on Mar 28, 2023

• tmp amplicon pivot

  jtsumner

  committed
  7608f1b

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Commits on Feb 16, 2023

• added special fastp for amplicon triming

  jtsumner

  committed
  bd4a6e9

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Commits on Feb 15, 2023

• added readQC analysis notebook

  jtsumner

  committed
  5d4ceff

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Commits on Feb 14, 2023

• debugging + assembly update

  jtsumner

  committed
  db4eb82

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Commits on Feb 13, 2023

• debugged multiqc

  jtsumner

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  f32e593

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• updated fastqc module + refactored

  jtsumner

  committed
  27b697f

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Commits on Feb 11, 2023

• added complexity filtering and merging options in readQC module + refactored

  jtsumner

  committed
  1a34c6a

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Commits on Feb 10, 2023

• general code clean up and assemblies take bowtie2_out + 2500 bp limit

  jtsumner

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  87d8b4f

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• updated gitignore

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  da7cd41

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Commits on Feb 8, 2023

• added kraken notebooks

  jtsumner

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  036e663

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Commits on Feb 7, 2023

• Refactored workflow names, added notebooks

  jtsumner

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  fbd3e8b

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Commits on Feb 5, 2023

• moved notes around

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  e89653a

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