Dev metagenomics low biomass bn#195
Merged
bnovak32 merged 13 commits intonasa:DEV_Metagenomics_low_biomassfrom Mar 19, 2026
Merged
Dev metagenomics low biomass bn#195bnovak32 merged 13 commits intonasa:DEV_Metagenomics_low_biomassfrom
bnovak32 merged 13 commits intonasa:DEV_Metagenomics_low_biomassfrom
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- fixed spelling/typos across both documents
- Illumina updates
- removed remove human reads step and added reference to remove human
reads pipeline
- renumbered steps and fixed internal links
- add missing suffixes - fix incorrect suffixes - remove unneeded file suffixes (only needed on published files) - remove unused samtools index step in Assembly-based processing
- changed csv to tsv - updated feature_decontam method to create correctly named files
- removed humann from software table in long read pipeline - updated output naming for humann outputs from path- to pathway-
- fix broken links - add missing filtering steps in Assembly-based processing - synchronize assembly-based downstream processing with workflow draft - standardize naming of output files in Assembly-based downstream processing
- Added top50 heatmap pngs generation - Fixed defintions for heatmaps and contig-level output - added note about decontaminated plots and species tables only being present when 1 or more contaminants found - fixed assay suffixes in GL-DPPD-7116
- reorganize R code - update thresholds to match current implementation
- update kraken2 build commands to use k2 wrapper and add pointers to RemoveHumanReads pipeline - refactor R code in long-read pipeline to match short-read and workflow implementation - update thresholds and defaults to match current implementation
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Updates to low biomass pipeline docs