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Update README.md #63

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Expand Up @@ -45,84 +45,6 @@ issue.
| Maintainer | [Dakota Howard](https://github.com/dthoward96) |
| Back-Up | [Reina Chau](https://github.com/rchau88), [Brian Lee](https://github.com/leebrian) |

## 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](https://account.ncbi.nlm.nih.gov/).

2. Required for CDC users and highly recommended for others is creating
a center account for your institution/lab [NCBI Center Account
Instructions](https://submit.ncbi.nlm.nih.gov/sarscov2/sra/#step6).
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](https://submit.ncbi.nlm.nih.gov).
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](https://account.ncbi.nlm.nih.gov/).

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](https://submit.ncbi.nlm.nih.gov/sarscov2/genbank/#step5)
For further questions contact
<a href="mailto:[email protected]">[email protected]</a>
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.

<!-- end list -->

- **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 supports upload to EpiFlu (**Influenza A Virus**), EpiCoV
(**SARS-COV-2**), EpiPox (**Monkeypox**), and EpiArbo (**Arbovirus**).
Before uploading, submitter needs to

1. Have a GISAID account. To sign up, visit [GISAID
Platform](https://gisaid.org/).

2. Request a client-ID for your specified Epi(Flu/CoV/Pox/Arbo)
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
<a href="mailto:[email protected]" >[email protected]</a> 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
<a href="https://cdcgov.github.io/seqsender/articles/images/fluCLI_download.png" target="_blank">EpiFlu</a>
or
<a href="https://cdcgov.github.io/seqsender/articles/images/covCLI_download.png" target="_blank">EpiCoV</a>
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.

![](man/figures/gisaid_cli_dir.png)

## Code Attributions

Dakota Howard and Reina Chau for majority of the code base with input
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