Home

#should add images later #

Sequence Read Archive (SRA) Submission The NCBI Sequence Read Archive (SRA) is the largest publicly available repository of high throughput sequencing data. Here, I present my personal experience of uploading raw sequences on this repository. For more details, I encourage you to consult the submission portal guide, quick start guide, and file upload options. Before starting the submission, you can prepare your personal information, general information about the project and fundings, and the metadata and sample attribute tables. SRA autosaves all the information you provide so you may leave your submission at any step and come back later to complete it. The submission steps are as follows: Page 1 - Submitter

Page 2 - General info

Page 3 - Project info

Page 4 - Biosample type

Page 5 - Biosample attributes The column titles in this section change depending on the sample type. The fields marked with * are required (copy-paste or upload the .tsv file). If you have more measured attributes other than what is in the table or columns with different titles, you may add those columns to the end of the table. Here, I present examples of two types of samples, metagenome or environmental sample and human sample. Metagenome or environmental sample:

Human sample:

Note: Before depositing human data into the public SRA database, make sure that you have consent from the donating individual to make this data available in an unprotected database. Do not transmit unconsented human data intended for dbGaP submissions to the public SRA database. Please refer to dbGaP submission Guide. Human metagenomic studies may contain human sequences and require that the donor provide consent to archive their data in an unprotected database. If you would like to archive human metagenomic sequences in the public SRA database, you may contact NCBI prior to submission. Page 6 - SRA metadata In this section, you provide the necessary information related to your metadata. The fields marked with * are required (copy-paste or upload the .tsv file).

Page 7 - Files There are different ways to upload raw read files. I chose the FTP upload using FileZilla (it’s free) since it was the most straightforward. Files should be uploaded in one folder and can be compressed (gzip, bzip2 or in a tar archive), although it is not required. Connect to NCBI through FileZilla:

Host: ftp-private.ncbi.nlm.nih.gov Username: use provided username Password: use provided password

In the “Remote site” bar, add this manually: uploads/[email protected]_xxxxx (use provided address) Make a new folder in the “uploads” folder, which will be your submission directory where you will transfer all the raw sequence files. Drag the files from the local site to the new folder on the Remote site (this will take some time, depending on the size of your files and your internet upload speed).

Finally, it will take about 10 minutes for uploaded files to become available on SRA.

Load folder and go to the next (last) page to review your submission or simply auto finish it.