How to preload files

One option for batch or single-genome submissions is to preload the genome files before beginning the submission, rather than uploading them in the browser during the submission. You can preload using Aspera, the FTP protocol or Filezilla, as described below.

To preload files, go to the genome submission page. The first time that you preload files, you need to:

• Open the "Command line options to preload files"
• Click the button to request a preload folder.
• Open the appropriate option to upload via Aspera or FTP
• Follow the instructions that appear (The instructions for Aspera and FTP instructions below are the same as those on the submission page.)

NOTE: You only need to request a preload folder once. After that, the "Aspera command line upload" and "FTP upload to preload files" options will be present on the page, so you only need to follow the appropriate directions there.

NOTE: It takes approximately 15 minutes after file upload has completed before the files are available in your submission.

FYI, detailed instructions for using the preload option for SRA submissions is at https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sra/docs/submitspfiles/. The instructions are analogous for genome submissions, but refer to the SRA submission page rather than the genome submission page .

Aspera command line instructions

You may use the following command to upload files via Aspera command line:

ascp -i <path/to/key_file> -QT -l100m -k1 <path/to/folder-with-file(s)> subasp@upload.ncbi.nlm.nih.gov:uploads/<user@email.com_xxxxx>

Please note:

• <user@email.com\_xxxxx> is your personal folder generated for you;
• <path/to/key\_file> must be an absolute path, e.g.: /home/keys/aspera.openssh;
• <key\_file> is provided upon your clicking on "Get the key file" link.

NOTE: The subfolder <folder-with-file(s)>; will be created automatically by Aspera within your root pre-upload folder. This is a folder that will be available for selection in the course of the submission. The folder is a temporary holding area and the files will be removed shortly after the submission is finished (the button Submit is clicked). Do not upload complex directory structures and files that do not contain sequence data!

FTP instructions

You can upload your files to the FTP server using the credentials below: - Address: ftp-private.ncbi.nlm.nih.gov - Username: subftp - Password: provided on the page.

After you login, navigate to your account folder: - cd uploads/xxxxx

Create a folder (use command mkdir) for your data within your FTP folder: - mkdir *your_directory*

Navigate to this directory and deposit the genome files: - cd *your_directory* - put file_name

NOTES:

• If you upload your files in your root directory, you will not be able to see them or to select them during the genome submission.

• The folder is a temporary holding area and the files will be removed after the submission is finished (the button Submit is clicked) OR you delete the submission. Do not upload complex directory structures and files that do not contain sequence data! ALL the files in this directory will be part of the submission, so do not include extraneous files.

General instructions on how to use FTP and Aspera for first time users are given here: SRA file upload options (please note that credentials are different).

FileZilla

When using FileZilla to upload the file you need to paste your account folder into the "Remote Site" box on the right hand side of FileZilla interface (outlined in red) and hit "Enter". From there you can create your data folder for your submission(s). Until you do this, you will see a message stating "550: Permission denied" or "Fail to read the directory listing". We prevent directory listing in the default sign in folder for security reasons. See more Filezilla details at https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sra/docs/submitfiles/.

You can view analogous instructions at https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sra/docs/submitspfiles /.

The next step- Create the submission

Start a New submission on https://submit.ncbi.nlm.nih.gov/subs/genome Provide the requested information, answer the questions, and upload the Genome Info file (for batch submissions only) Choose I have all files preloaded for this submission (NOTE: It takes approximately 15 minutes after file upload has completed before the files are available here.) Click on the button Select Submission Folder . Select the folder from the list. Click on the button Use selected folder . Click on the button Continue at the bottom of the page Review the submission's summary and click Submit.

See the genome submission instructions for what happens next .