Protocol for upload genomic data to NCBI
- Create a SRA project (thi)
- https://submit.ncbi.nlm.nih.gov/subs/sra/ [New Submission]
- Create new BioProject and Biosamples in the same SRA project (later you can access to theirs respective ids)
- Fill the excel data for the pathogens and save as a tab delimited file
- Fill the excel with the SRA Metadata and save as a tab delimited file
- ftp upload for the reads (>300 mb)
- Access to NCBI ftp server:
ftp -i ncbi_ftp_server(the user and password are in the login page of your submission portal) - cd to upload folders and create a subfolder with a meaningful name (mkdir)
mput *files(this upload the files to ftp server)- Wait
- Create a WGS project
- https://submit.ncbi.nlm.nih.gov/subs/wgs [New Submission]
- You gonna need
- Bioproject ID (this data are in the SRA submission portal)
- Biosample ID (this data are in the SRA submission portal)
- Assembly method and version
- Coverage of the sequence
- Sequencing Technology
- The contig file
- Authors for the sequence and a reference title.
- Upload the contig fasta file (min contig len > 200) (use perl script:
./removesmalls.pl 200 contigs.fasta > contigs_200.fasta)