IRIDA Testing Data Package ========================== This data package contains example data that can be used for testing IRIDA's data upload feature, and for evaluating pipeline execution. You should download the `.zip` file in this directory. What's in the package --------------------- This package contains a number of reference files (found in the `references` directory) and corresponding *simulated* Illumina MiSeq runs in the `miseq-run*` directories, either paired-end or single-end. You can find the reference genomes on NCBI: * `08-5923` Listeria monocytogenes 08-5923 * `08-5578` Listeria monocytogenes 08-5578 * `hcc23` Listeria monocytogenes HCC23 * `AE014613` Salmonella enterica subsp. enterica serovar Typhi Ty2 (AE014613.1) The paired-end reads were simulated using [ART](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278762/) with the following command (issued from within the root of this directory, or in the `miseq-run-small` directory): for i in references/* ; do b=`basename $i .fasta` art_illumina -i $i -na -l 250 -p -ss MS -f 20 -m 400 -s 20 \\ -o ${b}_S1_L001_ done The single-end directory simply contains a copy of the forward-strand reads from the paired-end directory. You can confirm the equality of the files using a checksum program like `md5sum`. Uploading this data to IRIDA ---------------------------- You have two options for uploading this data to IRIDA: 1. Using the [web interface](#using-the-web-interface), you can upload the files one at a time, or 2. Using the [uploader tool](#using-the-irida-uploader) you can upload the complete run directory as a single unit. ### Using the web interface If you want to upload individual files using the web interface, please follow the IRIDA user guide on uploading a new sequence file to a sample: ### Using the IRIDA uploader If you want to upload the entire set of files as a complete sequencing run, you should use the IRIDA uploader tool. Please follow the IRIDA user guide on uploading a sequencing run using the uploader tool: