Example: Running 16S Short-Read

#To test installation

cosmosid

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1. Uploading samples for 16S ASV analysis

1. In the command line, navigate to your directory containing paired-ended WGS samples in FASTQ format. CLI supports files of following extensions: ‘fasta’, ‘fna’, ‘fasta.gz’, ‘fastq’, ‘fq’, ‘fastq.gz’, ‘bam’, ‘sra’
2. Create a cloud directory for your uploads and grab the folder key
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   Ask AI

     cosmosid --api_key <YOUR_API_KEY> --base_url https://app.cosmosid.com mkdir --name 16S_project
   

   1. This command will produce a folder UUID that will be used for further commands.
   2. Example output: Folder 16S_project: 0e8ac013-07db-4ccf-a4ef-c22477556185 has been created
3. Upload your data to your new parent directory using the folder UUID and workflow command using the upload command:

cosmosid --api_key <YOUR_API_KEY> --base_url https://app.cosmosid.com upload \
  --file sample_R1.fastq.gz --file sample_R2.fastq.gz \
  --parent <FOLDER_UUID> \
  --type amplicon-16s \
  --wf ampliseq \
  --forward-primer <SEQUENCE> \
  --reverse-primer <SEQUENCE> \
  --dir $(pwd)

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2. Download results in .zip format

1. Check the list of samples and their statuses using the files command and grab the Sample UUID:
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   Ask AI

    cosmosid --api_key <YOUR_API_KEY> --base_url https://app.cosmosid.com files
      -- parent <FOLDER_UUID>
   

   OR Use the following command to export all sample UUIDs within your parent directory
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   Ask AI

   cosmosid --api_key <YOUR_API_KEY> --base_url https://app.cosmosid.com files --parent <FOLDER_UUID> -f csv | tail -n +3 | cut -f3 -d ‘,’ > 16s_ids.tsv
   

1. Select the sample UUID(s) and use it in the reports command to download results.
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   Ask AI

   cosmosid --api_key <YOUR_API_KEY --base_url https://app.cosmosid.com reports --id <SAMPLE_ID>
   

   OR Use the following command with the 16S_ids.tsv file to download all of your samples within your parent directory:

cat champ_ids.tsv | sed ‘s/”//g’ | while read line; do echo $line; cosmosid --api_key <YOUR_API_KEY> --base_url <https://app.cosmosid.com> reports --id $line; done