Submission Guide
-Toggling Submission:
-You will want to define whether to run the full pipeline with submission or without submission using the --submission flag. By default the pipeline will submit to GenBank and SRA. If you want to submit to only SRA, specify --genbank false --sra.
Submission Pre-requisites:
-Link to this guide and remove from previous section
-The submission component of the pipeline uses the processes that are directly integrated from SeqSender public database submission pipeline. It has been developed to allow the user to create a config file to select which databases they would like to upload to and allows for any possible metadata fields by using a YAML to pair the database's metadata fields with your personal metadata field columns. The requirements for this portion of the pipeline to run are listed below.
-(A) Create Appropriate Accounts as needed for the SeqSender public database submission pipeline integrated into TOSTADAS:
-NCBI: If uploading to NCBI archives such as BioSample/SRA/Genbank, you must complete the following steps:
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- Create a center account: Contact the following e-mail for account creation : sra@ncbi.nlm.nih.gov and provide the following information: -
- Suggested center abbreviation (16 char max) -
- Center name (full), center URL & mailing address (including country and postcode) -
- Phone number (main phone for center or lab) -
- Contact person (someone likely to remain at the location for an extended time) -
- Contact email (ideally a service account monitored by several people) -
- Whether you intend to submit via FTP or command line Aspera (ascp) -
- Gain access to an upload directory: Following center account creation, a test area and a production area will be created. Deposit the XML file and related data files into a directory and follow the instructions SRA provides via email to indicate when files are ready to trigger the pipeline. -
- GISAID: A GISAID account is required for submission to GISAID, you can register for an account at (https://www.gisaid.org/). Test submissions are first required before a final submission can be made. When your first test submission is complete contact GISAID at hcov-19@gisaid.org to receive a personal CID. GISAID support is not yet implemented but it may be added in the future. -
(B) Config File Set-up:
-The template for the submission config file can be found in bin/default_config_files within the repo. This is where you can edit the various parameters you want to include in your submission. Read more at the SeqSender docs.
-You can find more information on how to setup your own submission config and additional information on fields in the following guide: Submission Config Guide.
❗ Pre-requisite to submit to GenBank: Copy the program table2asn to your tostadas/bin directory by running the following lines of code:
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cd ./tostadas/bin/
-wget https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/linux64.table2asn.gz
-gunzip linux64.table2asn.gz
-mv linux64.table2asn table2asn
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Required Files for Submission
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- genbank -