diff --git a/README.md b/README.md index 206f94a..8e7dee7 100644 --- a/README.md +++ b/README.md @@ -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 - 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. - - - - - **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 - 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. - -![](man/figures/gisaid_cli_dir.png) - ## Code Attributions Dakota Howard and Reina Chau for majority of the code base with input