Freyja-SC2

Automated SRA downloading, processing and Freyja analysis pipeline for SARS-CoV-2 wastewater sequencing data.

Installation

git clone https://github.com/andersen-lab/Freyja-SC2.git
cd Freyja-SC2

Usage

nextflow run main.nf -entry [fetch|rerun_demix] -profile [docker|singularity] --accession_list [accession_list.csv] --output_dir [output_dir] --num_samples [num_samples]

Parameters

• -entry - The pipeline entry point.

  • fetch will download, process and run Freyja on the provided SRA accessions.

    • --sra_metadata - A CSV file containing a list of SRA accessions to download and process. The CSV file should have a header row, containing at least the following metadata fields:
      • accession - The SRA accession number (e.g. SRR1234567).
      • sample_status - The status of the sample (e.g. "to_run", "completed").
      • amplicon_PCR_primer_scheme - The amplicon primer scheme used for the sample (e.g. "ARTIC V4", ARTIC V5.3.2, unknown etc.)
    • --num_samples - The number of samples to process per run. (default: 100)

  • rerun_demix will run freyja demix step on previously generated variants output files in the provided variants directory. This is useful if you want to run Freyja on existing data with a different barcode set.

    • --variants_dir must contain files in the format [base_name].variants.tsv [base_name].depths.tsv for each sample.

  • --output_dir - The final output directory. Creates variants and demix subdirectories containing respective output files. (default: ./outputs)

Configuration

Addtional configuration options can be found in nextflow.config

Data Availability

freyja-sc2 is currently in the process of downloading and processing all publicly available SARS-CoV-2 wastewater data, fetched with the following search terms:

'(Wastewater[All Fields] OR wastewater metagenome[All Fields]) AND ("Severe acute respiratory syndrome coronavirus 2"[Organism] OR SARS-CoV-2[All Fields])

In addition, to the above search terms, we exclude accessions that don't meet the following metadata requirements:

• Missing collection date
• Missing catchment size (ww_population)
• Missing location (geo_loc_name)

To check the status of each accession, please refer to the sample_status column in data/all_metadata.tsv. All currently processed freyja outputs are publicly available via Google Cloud Storage at gs://outbreak-ww-data