How tomasdemelo/ww-genotyper works
WW-Genotyper processes wastewater sequence data into EV/NV genotypes and a longitudinal summary report. The documented workflow begins with FASTQ preprocessing, then analyzes combined FASTA sequences against reference databases, incorporates viral-load data, and reports abundance, mutation, and statistical results. The README also describes an optional ESM-2 mutation-scoring integration. The R scripts and shell scripts were not excerpted, so detailed internal calls and sequencing are not asserted; the main links below are supported by README statements.
Main entry points: WW_Genotyper-v11.R EV/NV genotyper · example_data Combined FASTA · FASTA-seq_condenser.sh FASTA condenser · EVminimap2.sh EV mapping
Components 16
Sequence preprocessing
- FASTA condenser
FASTA-seq_condenser.sh - EV mapping
EVminimap2.sh - NV mapping
NVminimap2.sh
Genotyping analysis
- EV/NV genotyper
WW_Genotyper-v11.R - Windows genotyper
WW_Genotyper-v11_Windows.R - Validation analysis
WW_Genotyper-v2_Validation.R - Genotypes and variants
WW_Genotyper-v11.R - Abundance normalization
WW_Genotyper-v11.R - Longitudinal statistics
WW_Genotyper-v11.R
Mutation triage
- ESM-2 scoring
score_mutation.py - ESM-2 model
Results and inputs
- Combined FASTA
example_data - Reference sequences
references - RT-qPCR data
RT-qPCR_data.xlsx - Summary report
WW_Genotyper-v11.R
Other components
- Analyst
Connections 18
- Analyst → FASTA condenser: preprocesses reads
README.md - Analyst → EV mapping: preprocesses reads
README.md - Analyst → NV mapping: preprocesses reads
README.md - FASTA condenser → Combined FASTA: produces sequences
README.md - EV mapping → Combined FASTA: produces sequences
README.md - NV mapping → Combined FASTA: produces sequences
README.md - Analyst → EV/NV genotyper: runs analysis
README.md - Combined FASTA → EV/NV genotyper: analyzed by
README.md - Reference sequences → EV/NV genotyper: reference database
README.md - RT-qPCR data → EV/NV genotyper: viral-load input
README.md - Analyst → Windows genotyper: runs on Windows
README.md - Analyst → Validation analysis: validates genotyping
- EV/NV genotyper → Genotypes and variants: calls genotypes
README.md - EV/NV genotyper → Abundance normalization: normalizes abundance
README.md - EV/NV genotyper → Longitudinal statistics: models trends
README.md - EV/NV genotyper → ESM-2 scoring: scores variants
README.md - ESM-2 scoring → ESM-2 model: loads model
score_mutation.py - EV/NV genotyper → Summary report: generates report
README.md