About

RESPICAT is a genome catalogue of human respiratory tract prokaryotes. The catalogue provides dereplicated metagenome-assembled genomes (MAGs), genome-level metadata, taxonomic annotations, genome quality summaries, checksum files, and helper scripts for accessing the RESPICAT v1.0 release.

RESPICAT v1.0 genome archive

The RESPICAT MAG FASTA files are distributed as a compressed archive:

RESPICAT_MAGs_v1.0.tar.gz

The genome archive will be deposited in an external archival repository. The final download link will be added here after deposition:

Genome archive: RESPICAT_MAGs_v1.0.tar.gz

After extraction, the archive contains public MAG FASTA files named with stable RESPICAT identifiers:

RESPICAT_MAG_000001.fna
RESPICAT_MAG_000002.fna
RESPICAT_MAG_000003.fna
...

Contig identifiers inside each FASTA file follow the same public naming scheme:

>RESPICAT_MAG_000001_contig_000001
>RESPICAT_MAG_000001_contig_000002

Repository structure

The GitHub repository contains metadata, documentation, checksums, and reproducible helper scripts for accessing the RESPICAT v1.0 MAG catalogue.

RESPICAT GitHub repo
├── README.md
├── metadata/
│   ├── RESPICAT_MAG_metadata_v1.0.tsv
│   ├── RESPICAT_MAG_taxonomy_v1.0.tsv
│   ├── RESPICAT_MAG_quality_summary_v1.0.tsv
│   └── RESPICAT_MAG_id_mapping_v1.0.tsv
├── scripts/
│   ├── download_RESPICAT_MAGs.sh
│   ├── verify_checksums.sh
│   └── prepare_RESPICAT_MAG_release.R
├── checksums/
│   └── RESPICAT_MAGs_v1.0.sha256
└── docs/
    └── RESPICAT_MAG_catalog_description_v1.0.md

Public release files

Metadata files

File	Description
metadata/RESPICAT_MAG_metadata_v1.0.tsv	Main MAG-level metadata table containing public MAG IDs, FASTA filenames, basic provenance, taxonomy, and genome quality metrics.
metadata/RESPICAT_MAG_taxonomy_v1.0.tsv	Taxonomy-only table with public MAG IDs and taxonomic ranks.
metadata/RESPICAT_MAG_quality_summary_v1.0.tsv	Genome quality summary table containing completeness, contamination, strain heterogeneity, genome size, N50, and dereplication score.
metadata/RESPICAT_MAG_id_mapping_v1.0.tsv	Mapping table linking public RESPICAT MAG IDs to original internal MAG identifiers, original FASTA filenames, ATLAS batch IDs, and original MAG labels.

Checksum file

File	Description
checksums/RESPICAT_MAGs_v1.0.sha256	SHA-256 checksum file for validating the downloaded RESPICAT MAG genome archive.

Scripts

File	Description
scripts/download_RESPICAT_MAGs.sh	Helper script for downloading the RESPICAT MAG archive after the external archive link is available.
scripts/verify_checksums.sh	Helper script for validating the downloaded genome archive using the SHA-256 checksum file.
scripts/prepare_RESPICAT_MAG_release.R	R script used to prepare public MAG identifiers, rename FASTA files, rename contig headers, and generate public metadata files.

Downloading the helper scripts

The RESPICAT helper scripts are available in the scripts/ directory.

scripts/
├── download_RESPICAT_MAGs.sh
├── verify_checksums.sh
└── prepare_RESPICAT_MAG_release.R

Option 1: Download from the browser

To download an individual script:

1. Open the scripts/ directory.
2. Click the script you want to download, for example download_RESPICAT_MAGs.sh.
3. Click Raw.
4. Right-click on the page and choose Save as.
5. Save the file with the same filename, for example: download_RESPICAT_MAGs.sh

Option 2: Download scripts from the command line

Users familiar with the terminal can download the scripts directly.

# Download the genome archive helper script
curl -L -o download_RESPICAT_MAGs.sh \
  https://raw.githubusercontent.com/CME-lab-research/RESPICAT/main/scripts/download_RESPICAT_MAGs.sh

# Download the checksum verification script
curl -L -o verify_checksums.sh \
  https://raw.githubusercontent.com/CME-lab-research/RESPICAT/main/scripts/verify_checksums.sh

After downloading, make the scripts executable:

chmod +x download_RESPICAT_MAGs.sh
chmod +x verify_checksums.sh

Then run:

./download_RESPICAT_MAGs.sh
./verify_checksums.sh

Documentation

File	Description
docs/RESPICAT_MAG_catalog_description_v1.0.md	Detailed description of the RESPICAT MAG catalogue, public identifier scheme, metadata fields, and release contents.

Public identifier scheme

Each dereplicated MAG receives one stable public MAG identifier:

RESPICAT_MAG_000001

Each contig within a MAG receives a contig-level identifier derived from the corresponding public MAG ID:

RESPICAT_MAG_000001_contig_000001

The file metadata/RESPICAT_MAG_id_mapping_v1.0.tsv links public RESPICAT MAG IDs to the original internal genome identifiers and original FASTA filenames.

Verifying downloaded genome files

After downloading RESPICAT_MAGs_v1.0.tar.gz, verify the archive with the provided checksum file:

sha256sum -c checksums/RESPICAT_MAGs_v1.0.sha256

Alternatively, use the helper script:

# Run as
bash scripts/verify_checksums.sh

# Or run with explicit paths
bash verify_checksums.sh RESPICAT_MAGs_v1.0.tar.gz checksums/RESPICAT_MAGs_v1.0.sha256

It supports both sha256sum on Linux and shasum -a 256 on macOS.

Data availability

Raw sequencing reads are available through ENA under accession PRJEB96845.

Reused public metagenomic datasets were retrieved from ENA/SRA. The list of reused BioProjects is provided in the manuscript supplementary tables.

The RESPICAT v1.0 MAG genome archive will be made available through an external archival repository:

Archive link: Zenodo DOI

Citation

Citation information will be added after publication or public release of the corresponding manuscript/preprint.