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Add low biomass pipelines and update standard metagenomics pipeline - #197

Merged

bnovak32 merged 50 commits into

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DEV_Metagenomics_low_biomass

Apr 18, 2026

Merged

Add low biomass pipelines and update standard metagenomics pipeline#197
bnovak32 merged 50 commits into
masterfrom
DEV_Metagenomics_low_biomass

Commits on Sep 8, 2025
- Added first draft of low-biomass ppl
  bnovak32
  committed
  fb46143
- Fixed Assembly section numbering
  bnovak32
  committed
  60fb1fc
Commits on Sep 19, 2025
- Added read-based decontamination
  bnovak32
  committed
  5821e1d
- added missing parameter definition
  bnovak32
  committed
  a332edf
Commits on Sep 22, 2025
- Adding Low Biomass Nanopore Metagenomics Pipeline document
  asaravia-butler
  authored
  52abb0c
Commits on Sep 30, 2025
- Update Low Biomass pipeline draft (#176)
  bnovak32
  authored
  02f19f8
Commits on Oct 2, 2025
- added decontamination and visualization steps, and fixed broken links
  olabiyi
  committed
  6e6924c
- fixed broken links
  olabiyi
  committed
  0e0cf11
- fixed broken links
  olabiyi
  committed
  2e4f7f1
Commits on Oct 6, 2025
- made edits to functions and the overall document
  olabiyi
  committed
  9c150ef
Commits on Oct 8, 2025
- Merge pull request #178 from olabiyi/DEV_Metagenomics_low_biomass
  asaravia-butler
  authored
  cefd6c2
Commits on Oct 9, 2025
- fixed run_decontam()
  olabiyi
  committed
  519b987
- Changed how filtered table is generated for kraken and kaiju
  olabiyi
  committed
  ba251b7
- Changed how filtered table is generated for kraken and kaiju
  olabiyi
  committed
  069fb14
- Fixed decontamination_table bug
  olabiyi
  committed
  285abb7
Commits on Oct 10, 2025
- Fixed bug with reading and writing species table
  olabiyi
  committed
  f843916
Commits on Oct 13, 2025
- R code bug fixes
  asaravia-butler
  authored
  b6e709e
Commits on Nov 13, 2025
- Updates to the dev low biomass pipeline document GL-DPPD-7116
  asaravia-butler
  authored
  96df97f
Commits on Nov 19, 2025
- Update GL-DPPD-7110-A_annotations.csv
  bnovak32
  committed
  82a7043
- Update humann3.yaml
  bnovak32
  committed
  a93c9c4
Commits on Dec 21, 2025
- Updated assay suffixes
  bnovak32
  committed
  9c1b618
Commits on Jan 24, 2026
- Updates to Low-biomass pipeline docs
  bnovak32
  committed
  c886d8d
Commits on Jan 25, 2026
- Updated assembly decontamination and heatmap section
  bnovak32
  committed
  a196c7a
Commits on Jan 26, 2026
- Finished Illumina low-biomass pipeline draft
  bnovak32
  committed
  614c145
- Update GL-DPPD-7116.md (#188)
  asaravia-butler
  authored
  ef65dd5
Commits on Jan 27, 2026
- pipeline document updates through step 8c
  bnovak32
  committed
  661fbac
- Update GL-DPPD-7117
  bnovak32
  committed
  cb75153
- update get_abundant_features functions docs
  bnovak32
  committed
  e7cd701
Commits on Jan 28, 2026
- Dev metagenomics low biomass - nanopore updates through step 9c (#190)
  asaravia-butler
  authored
  2d7d797
- Finish renumbering and minor formatting edits
  bnovak32
  committed
  4b21d2d
- typo fix on GL-DPPD-7117.md
  asaravia-butler
  authored
  12305ef
- typo fix on GL-DPPD-7117.md
  asaravia-butler
  authored
  3965569
Commits on Jan 29, 2026
- formatting updates to GL-DPPD-7116.md
  asaravia-butler
  authored
  3c08da6
- Formatting updates to GL-DPPD-7117.md
  asaravia-butler
  authored
  341b900
Commits on Mar 19, 2026
- Dev metagenomics low biomass bn (#195)
  bnovak32
  authored
  7366989
- Add low-biomass README
  bnovak32
  committed
  65ae99c
Commits on Mar 23, 2026
- updated Metagenomiocs Workflow links
  bnovak32
  committed
  4f66432
- added human functional profiling to long-read pipeline
  bnovak32
  committed
  03cbf07
Commits on Mar 24, 2026
- updated Biyi's team designation
  bnovak32
  committed
  19747ec
Commits on Mar 25, 2026
- Added GL-DPPD-7107-B doc
  bnovak32
  committed
  d13b7ba
- updated low-biomass README with workflow doc link
  bnovak32
  committed
  1a1ddd9
- updated header
  bnovak32
  committed
  a779e3c
Commits on Mar 26, 2026
- Update GL-DPPD-7107-B.md
  bnovak32
  authored
  5367c7e
Commits on Apr 1, 2026
- formatting and software version updates
  bnovak32
  committed
  468915b
Commits on Apr 4, 2026
- updated bbduk to BBTools
  bnovak32
  committed
  69b3f0e
Commits on Apr 15, 2026
- Final updates
  bnovak32
  committed
  a3ad2d6
- Updated Metagenomics READMEs and added NF_Metagenomics repository links (#198)
  bnovak32
  authored
  e21868f
- Updated Metagenomics workflow name (#199)
  bnovak32
  authored
  a8ca305
Commits on Apr 18, 2026
- Update README.md
  bnovak32
  authored
  44cce13
- Update README.md
  bnovak32
  authored
  ee00d2b

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