Quick Start

The following steps will download real wastewater datasets and analyze them using WEPP.

Example - 1: RSV-A Dataset (Runs Quickly: Under 10 minutes on 32 cores)

Step 1: Download the RSV-A test dataset

mkdir -p data/RSVA_real
cd data/RSVA_real
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR147/011/ERR14763711/ERR14763711_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR147/011/ERR14763711/ERR14763711_2.fastq.gz https://hgdownload.gi.ucsc.edu/hubs/GCF/002/815/475/GCF_002815475.1/UShER_RSV-A/2025/04/25/rsvA.2025-04-25.pb.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/815/475/GCF_002815475.1_ASM281547v1/GCF_002815475.1_ASM281547v1_genomic.fna.gz
gunzip GCF_002815475.1_ASM281547v1_genomic.fna.gz 
mv ERR14763711_1.fastq.gz ERR14763711_R1.fastq.gz
mv ERR14763711_2.fastq.gz ERR14763711_R2.fastq.gz
cd ../../

This will save the datasets on a separate data/RSVA_real folder within the repository.

Step 2: Run the pipeline

snakemake --config DIR=RSVA_real FILE_PREFIX=test_run TREE=rsvA.2025-04-25.pb.gz REF=GCF_002815475.1_ASM281547v1_genomic.fna CLADE_LIST=annotation_1 CLADE_IDX=0 DASHBOARD_ENABLED=True --cores 32 --use-conda

Step 3: Analyze Results

All results generated by WEPP are available in the results/RSVA_real directory. These include haplotype and lineage abundances, associated uncertain haplotypes, and the potential haplotypes corresponding to each detected unaccounted allele.

Note

⚠️ Make sure port forwarding is enabled when accessing services on external servers.

Example - 2: SARS-CoV-2 Dataset (Longer Runtime: ~20 minutes on 32 cores)

Step 1: Download the SARS-CoV-2 test dataset

mkdir -p data/SARS_COV_2_real
cd data/SARS_COV_2_real
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR185/041/SRR18541041/SRR18541041_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR185/041/SRR18541041/SRR18541041_2.fastq.gz https://hgdownload.gi.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/2021/12/05/public-2021-12-05.all.masked.pb.gz
mv SRR18541041_1.fastq.gz SRR18541041_R1.fastq.gz
mv SRR18541041_2.fastq.gz SRR18541041_R2.fastq.gz
cp ../../NC_045512v2.fa .
cd ../../

This will save the datasets on a separate data/SARS_COV_2_real folder within the repository.

Step 2: Run the pipeline

snakemake --config DIR=SARS_COV_2_real FILE_PREFIX=test_run TREE=public-2021-12-05.all.masked.pb.gz REF=NC_045512v2.fa DASHBOARD_ENABLED=True --cores 32 --use-conda

Step 3: Analyze Results

All results generated by WEPP are available in the results/SARS_COV_2_real directory. These include haplotype and lineage abundances, associated uncertain haplotypes, and the potential haplotypes corresponding to each detected unaccounted allele.

Note

⚠️ Make sure port forwarding is enabled when accessing services on external servers.