Hello everyone, I am developing a Nextflow pipeline that processes data from raw FASTQ files through to downstream analysis for both whole genome sequencing (isolate data) and shotgun metagenomics. For publication and reproducibility, I am looking for publicly available test datasets (preferably small to moderate size) that include: • Paired-end WGS isolate data • Shotgun metagenomic sequencing data The organism is not critical, but the data should be well-documented and suitable for benchmarking a full pipeline. I would appreciate any recommendations for reliable sources (e.g., specific studies, accession numbers, or curated benchmark datasets). Many thanks in advance.

For shotgun metagenomics see CAMI: https://cami-challenge.org/cami-ii/

The NCBI sequence read archive should have WGS data, but I have no idea how to find a smallish one with good quallity (except trying several). You can of course always downsample, but that makes it harder for others to reproduce. WGS from human should really be protected in dbGaP (except cell lines, I guess), but mouse should be accessible for everyone.