How pacificbiosciences/pb-metagenomics-tools works
This repository is a collection of Snakemake workflows and companion utilities for HiFi metagenomics, not one single analysis pipeline. Its main user workflows produce quality-filtered MAGs, compare and consolidate MAG sets, or profile taxa from reads using Sourmash, DIAMOND/MEGAN, or minimap2/MEGAN. Separate scripts convert profiling outputs into standard reports and compare those reports. The README documents the major stages and outputs; sampled source supports selected report-conversion and filtering behavior, so unsampled workflow wiring is represented only at the documented level.
Main entry points: Snakefile-hifimags.smk MAG workflow · Snakefile-sourmash Sourmash workflow · Snakefile-diamond-megan.smk DIAMOND MEGAN workflow · Snakefile-minimap-megan Minimap MEGAN workflow
Components 27
MAG recovery
- MAG workflow
HiFi-MAG-Pipeline/Snakefile-hifimags.smk - Long-contig protection
HiFi-MAG-Pipeline/Snakefile-hifimags.smk - Binning and merge
HiFi-MAG-Pipeline/Snakefile-hifimags.smk - MAG QC and taxonomy
HiFi-MAG-Pipeline/Snakefile-hifimags.smk - MAGs and summaries
HiFi-MAG-Pipeline/scripts/MAG-Summary.py
MAG comparison
- Mirror workflow
pb-MAG-mirror/Snakefile-pb-mag-mirror.smk - Filter bin sets
pb-MAG-mirror/scripts/Filter-Checkm2-Bins.py - Compare bins
pb-MAG-mirror/scripts/Perform-bin-comparisons.py - Consolidated MAG set
pb-MAG-mirror/scripts/Copy-consolidated-bins.py
Taxonomic profiling
- Sourmash workflow
Taxonomic-Profiling-Sourmash/Snakefile-sourmash - Sourmash profile
Taxonomic-Profiling-Sourmash - DIAMOND MEGAN workflow
Taxonomic-Profiling-Diamond-Megan/Snakefile-diamond-megan.smk - Minimap MEGAN workflow
Taxonomic-Profiling-Minimap-Megan/Snakefile-minimap-megan - Alignment and classification
Taxonomic-Profiling-Diamond-Megan - Taxonomy databases
- Taxonomic and functional reports
Taxonomic-Profiling-Diamond-Megan
Report utilities
- Format converters
pb-metagenomics-scripts/Convert-to-kreport-mpa - NCBI taxonomy lookup
- Compare kreports
pb-metagenomics-scripts/Compare-kreport-taxonomic-profiles - Standard reports and plots
pb-metagenomics-scripts/Compare-kreport-taxonomic-profiles
Other components
- Analyst
- HiFi assembly
- HiFi reads
- MEGAN-LR
- Sourmash
- Report user
- Profiler outputs
Connections 37
- Analyst → MAG workflow: runs
- HiFi assembly → MAG workflow: provides assembly
- MAG workflow → Long-contig protection: protects contigs
- MAG workflow → Binning and merge: bins and merges
- MAG workflow → MAG QC and taxonomy: runs QC
- MAG workflow → MAGs and summaries: produces
- Long-contig protection → Binning and merge: passes contigs
- Binning and merge → MAG QC and taxonomy: passes bins
- MAG QC and taxonomy → MAGs and summaries: records quality
- Analyst → Mirror workflow: runs
- Mirror workflow → Filter bin sets: filters bins
- Mirror workflow → Compare bins: compares sets
- Filter bin sets → Compare bins: provides passing bins
- Compare bins → Consolidated MAG set: consolidates sets
- HiFi reads → Sourmash workflow: provides reads
- Analyst → Sourmash workflow: runs
- Sourmash workflow → Sourmash: classifies
- Sourmash → Taxonomy databases: queries
- Sourmash workflow → Sourmash profile: writes profile
- HiFi reads → DIAMOND MEGAN workflow: provides reads
- Analyst → DIAMOND MEGAN workflow: runs
- DIAMOND MEGAN workflow → Alignment and classification: aligns and classifies
- Alignment and classification → MEGAN-LR: summarizes
- MEGAN-LR → Taxonomy databases: uses annotations
- DIAMOND MEGAN workflow → Taxonomic and functional reports: produces reports
- HiFi reads → Minimap MEGAN workflow: provides reads
- Analyst → Minimap MEGAN workflow: runs
- Minimap MEGAN workflow → Alignment and classification: aligns reads
- Alignment and classification → MEGAN-LR: summarizes
- Minimap MEGAN workflow → Taxonomic and functional reports: produces reports
- Report user → Format converters: requests conversion
- Profiler outputs → Format converters: provides input
- Format converters → NCBI taxonomy lookup: resolves lineages
- Format converters → Standard reports and plots: writes reports
- Report user → Compare kreports: requests comparison
- Profiler outputs → Compare kreports: provides kreports
- Compare kreports → Standard reports and plots: creates plots