• Created: 20 March, 2022
  • Update: 15 July, 2022

IBDC has developed a separate track for the submission of Covid-19 sequencing data at the
Indian Nucleotide Data Archive - Controlled Access (INDA-CA).

SOP Document for submission in PDF document

STEP 1: User registration

In order to submit COVID19 data sets, the user must register at INDA-CA.

  1. Click on the 'Register' button on the top panel on the INDA-CA homepage.
  2. Provide all the relevant details.
  3. All new user accounts needs to be activated after verification by IBDC staff. An email would be sent confirming the account activation at the registered email.

STEP 2: Select data submission track

  1. Visit IBDC website (www.ibdc.rcb.res.in) and click on 'INSACOG LOGO' or directly go to INDA-CA home page (skip to step 3).
  2. Select 'INDA-CA' on the next page.
  3. Select 'Template-based submission (INSACOG)' track within the box .
  4. Use login credentials provided by IBDC staff to login.

STEP 3: Data Submission

Submit data using the 'Template-based submission' track

  1. Log in to the 'Template Based submission' track using the login credentials received from IBDC.
  2. Download the template 'MS Excel' by clicking on the 'MetaData-INSACOG-template' link provided on the dashboard (Left panel). Fill in the metadata for multiple samples in the template file.
  3. Register 'Study': Register a study by providing relevant details.
  4. Upload Metadata: Click the link "Upload metadata" on the left panel of the dashboard.
    1. Select an appropriate 'Study' to which the data has to be submitted.
    2. Subsequently, select the appropriate 'metadata file'.
    3. Click on the 'Upload and Save button'

    If fields of the metadata file are as per format a success message will be displayed on the page.
    If any discrepancy is found an appropriate message will be displayed and the user has to correct the file and re-upload.

    Important points:
    1. The metadata template downloaded should be filled in according to the headers.
    2. Some fields are mandatory which have to be filled and it is advised not to edit the first two lines of the metadata template.
    3. Following fields are mandatory: 'Virus name', 'Collection Date',State','Sequencing Technology', 'Sample id given by the sample provider', 'Filename1' ,'md5sum1' and 'Strategy'.
      1. Virus name should be unique, duplicate entries will not be taken.
      2. Please enter the date in a uniform format of "dd/mm/yyyy" or "dd-mm-yyyy" in Collection date and Last vaccinated fields .
      3. Filename1 (Raw data filename) should be given with the extension for example "Filename.fastq.gz".
      4. Please do not enter text or any other characters in date fields.
      5. Please check for special character/tab/space before the dates in Collection date or in Last vaccinated column.
    4. The filename given in the metadata details should be exactly the same as the file which has to be uploaded in the next step.
    5. A valid Md5sumvalue for each file has to be given.
    6. Strategy field should be given either as single or paired. Values apart from this will not be considered.
  5. Raw Data Upload: Once the metadata has been uploaded successfully user can use the FTP details after clicking on the 'Raw Data upload' tab on the left panel on the dashboard. The filename should be the same as given in the metadata file uploaded.
    1. To upload the raw data you can use command line FTP or any third party file transfer FTP tools like Filezilla or Cyberduck.
    2. Please Change directory "cd" to a folder named "uploads" after loging in.
    3. Please create a new folder in "uploads" directory for new submission set and upload the data in the newly created folder.
  6. Map Uploaded files
    1. In this step user has to map the uploaded "raw data files" with the "metadata".
    2. User has to select the folder of the uploaded files and click on the button "Click here to Map All Uploaded Files".
      All the files with matching metadata will be mapped, a count of mapped and not mapped files will be shown on the page.
      IBDC accession will be provided when the files are mapped correctly for each uploaded sample.
Important points:
  1. The files will be mapped only if the filename given in the metadata matches the uploaded filenames.
  2. INDA-CA will verify the 'md5sum' value provided in the meta-data file with that of the data file. If they don't match user will be notified via email and the correct file has to be re-uploaded in the same folder.
Md5sum calculation in Terminal

(Windows User can terminal tools like MobaXterm)

  • Go to folder containing the fastq or fastq.gz files and open in terminal
  • Type the below given command in terminal

    md5sum *.fastq.gz &> md5sum.txt

    The mdsum.txt file will have all the md5sum saved

    For FTP submission using command line
  • Open terminal inside folder with fastq files.
  • ftp -i inda.rcb.ac.in

    Enter the FTP username and password when prompted

  • After successful login
  • cd uploads

  • Open terminal inside folder with fastq files.
  • ls

    (this gives list of folders available)

  • create a folder with the required name of your choice.
  • mkdir newfoldername

    (newfolder name can be of your choice )

  • change directory to newfoldername
  • cd newfoldername

  • create a folder with the required name of your choice.
  • mkdir newfoldername

  • type below command to upload files (change to fastq if without gz extention)
  • mput *.fastq.gz

    Kindly contact your institutional network team for allowing FTP port, incase of connection issue


    For any queries please write to us at indasupport@ibdc.rcb.res.in