How zhaoqing-wang/celljanus works
CellJanus deconvolves host and microbial signals from FASTQ, with bulk and single-cell workflows. The bulk route runs quality control, host alignment, unmapped-read extraction, microbial classification and abundance estimation, then produces summaries and visualizations. The scRNA-seq route tracks barcodes and UMIs to create cells-by-species results. Reference downloads support setup; the README also describes optional 16S cross-validation. The graph follows documented orchestration and sampled module behavior; some pipeline wiring and the 16S implementation were not sampled, so uncertain links are omitted.
Main entry points: pipeline.py Pipeline · classify.py Taxonomic analysis · cli.py CLI · align.py Host alignment
Components 19
Bulk workflow
- Read QC
celljanus/qc.py - Host alignment
celljanus/align.py - Unmapped reads
celljanus/extract.py - Taxonomic analysis
celljanus/classify.py - fastp
- Bowtie2
- samtools
- Kraken2
- Bracken
- Visualizations
celljanus/visualize.py
Single-cell workflow
- Barcode analysis
celljanus/scrnaseq.py - 16S validation
celljanus
References and results
- Reference download
celljanus/download.py - Host genome index
- Kraken2 database
- Analysis outputs
Other components
- Researcher
Connections 24
- Researcher → CLI: runs
- CLI → Pipeline: starts bulk
- Pipeline → Read QC: runs QC
- Pipeline → Host alignment: runs alignment
- Pipeline → Unmapped reads: runs extraction
- Pipeline → Taxonomic analysis: runs classification
- Pipeline → Visualizations: runs visualization
- Read QC → fastp: invokes
- Host alignment → Bowtie2: aligns with
- Host alignment → samtools: sorts and indexes
- Unmapped reads → samtools: extracts with
- Taxonomic analysis → Kraken2: classifies with
- Taxonomic analysis → Bracken: estimates abundance
- Host alignment → Host genome index: reads index
- Taxonomic analysis → Kraken2 database: reads database
- CLI → Barcode analysis: starts scRNA-seq
- Barcode analysis → Taxonomic analysis: runs Kraken2
- Barcode analysis → Analysis outputs: writes cell matrices
- Visualizations → Analysis outputs: writes plots
- Pipeline → Analysis outputs: writes reports
- CLI → Reference download: requests references
- Reference download → Host genome index: prepares index
- Reference download → Kraken2 database: downloads database
- Barcode analysis → 16S validation: optional validation