Public Database Submission Pipeline

Beta Version: 1.1.0. This pipeline is currently in Beta testing, and issues could appear during submission. Please use it at your own risk. Feedback and suggestions are welcome!

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Documentation

Overview

seqsender is a Python program that is developed to automate the process of generating necessary submission files and batch uploading them to NCBI archives (such as BioSample, SRA, and Genbank) and GISAID databases (e.g. EpiFlu and EpiCoV). Presently, the pipeline is capable of uploading Influenza A Virus (FLU) and SARS-COV-2 (COV) data. However, the dynamic nature of this pipeline can allow for additional uploads of other organisms in future updates or requests.

Contacts

Role	Contact
Creator	Dakota Howard, Reina Chau
Maintainer	Dakota Howard
Back-Up	Reina Chau, Brian Lee

Prerequisites

• NCBI Submissions

seqsender utilizes an UI-Less Data Submission Protocol to bulk upload submission files (e.g., submission.xml, submission.zip, etc.) to NCBI archives. The submission files are uploaded to the NCBI server via FTP on the command line. Before attempting to submit a submission using seqsender, submitter will need to

1. Have a NCBI account. To sign up, visit NCBI website.

2. Required for CDC users and highly recommended for others is creating a center account for your institution/lab NCBI Center Account Instructions. Center accounts allow you to perform submissions UI-less submissions as your institution/lab.

3. Required for CDC users and also recommended is creating a submission group in NCBI Submission Portal. A group should include all individuals who need access to UI-less submissions through the web interface with your center account. Each member of the group must also have an individual NCBI account. NCBI website.

4. Refer to this page for information regarding requirements for GenBank submissions via FTP only. This page applies only for COVID and Influenza NCBI GenBank FTP Submissions For further questions contact gb-admin@ncbi.nlm.nih.gov to discuss requirements for submissions.

5. Coordinate a NCBI namespace name (spuid_namespace) that will be used with Submitter Provided Unique Identifiers (spuid) in the submission. The liaison of spuid_namespace and spuid is used to report back assigned accessions as well as for cross-linking objects within submission. The values of spuid_namespace are up to the submitter to decide but they must be unique and well-coordinated prior to make a submission. For more information about these two fields, see BioSample / SRA / GENBANK metadata requirements.

• GISAID Submissions

seqsender makes use of GISAID’s Command Line Interface tools to bulk uploading meta- and sequence-data to GISAID databases. Presently, the pipeline only allows upload to EpiFlu (Influenza A Virus) and EpiCoV (SARS-COV-2) databases. Before uploading, submitter needs to

1. Have a GISAID account. To sign up, visit GISAID Platform.

2. Request a client-ID for EpiFlu or EpiCoV database in order to use its CLI tool. The CLI utilizes the client-ID along with the username and password to authenticate the database prior to make a submission. To obtain a client-ID, please email clisupport@gisaid.org to request. Important note: If submitter would like to upload a “test” submission first to familiarize themselves with the submission process prior to make a real submission, one should additionally request a test client-id to perform such submissions.

3. Download the EpiFlu or EpiCoV CLI from the GISAID platform and stored them in the destination of choice prior to perform a batch upload.

Here is a quick look of where to store the downloaded GISAID CLI package.

Requirement Files

Before submitters can perform a batch submission using seqsender, they must make sure the requirement files (such as config.yaml, metadata.csv, sequence.fasta, raw reads, etc.) are already prepared and stored in a submission directory of choice.

1. To prep for FLU submissions, select one of the databases below to get started:

BioSample
SRA
Genbank
GISAID

2. To prep for COV submissions, select one of the databases below to get started:

BioSample
SRA
Genbank
GISAID

Quick Start

• How to run seqsender locally
• How to run seqsender with Docker
• How to run seqsender with Compose
• How to run seqsender with Singularity

Code Attributions

Dakota Howard and Reina Chau for majority of the code base with input and testing from colleagues.

Public Domain Standard Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

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