CAMISIM hybrid time series data

CAMISIM was used to simulate Illumina and Nanopore reads for a time series based on the genome sources from the “CAMI II challenge toy mouse gut dataset” (Meyer et al., 2021), containing 791 genomes. For this, the most recent development version of CAMISIM at the time of preparing this data was used (available at https://doi.org/10.5281/zenodo.5137751). Two groups of samples were generated by using different CAMISIM seeds, each comprising a time series of four samples.

The sample sheet file (samplesheet.CAMISIM_hybrid.csv) can be used as direct input for the nf-core/mag pipeline, e.g. with the command:

> nextflow run nf-core/mag -r 2.1.0 -profile  --input https://zenodo.org/record/5155395/files/samplesheet.CAMISIM_hybrid.csv --coassemble_group

Note, in case of download problems, restarting the pipeline run with `-resume` or downloading the files beforehand and adjusting the paths in the sample sheet file should help.

See https://nf-co.re/mag for a comprehensive usage documentation.