Would appreciate any hints/information about submission of NGS data to public databases. In short – manuscript, describing abundance (in percent) of particular microbial groups in different samples based on 16S rRNA NGS (Illumina MiSeq) is ready for submitted to the journal. In the journal requirements, naturally, was mentioning that “manuscripts reporting sequence data must have GenBank accession numbers prior to submitting”. Questions are:
1. Is it really necessary to submit any data in this case – since only percent data (not sequences) are cited in the manuscript?
2. If it is necessary – how it should be done? – any specific tools for submitting NGS data? How data should be formatted? Any pipelines?
Hi German,
since all your results are based on NGS data, these data need to be accessible to everyone, but almost the reviewers to begin. There are few databases to accept your data, try the NCBI one in which I never had problem (https://www.ncbi.nlm.nih.gov/geo/info/seq.html). it's free, fast and reliable, and easy to manage the access.
fred
Hi.
Follow the webpage : https://www.ncbi.nlm.nih.gov/guide/howto/submit-sequence-data/
This gives you idea about how to submit the sequences.
Once submitted, NCBI will look into the data and after approval from their side you can get the accession codes.
Thanks,
Hi German Jurgens
For your first question, I think you need to submit the data, in this case fastq files, although you are planning to present the abundance data because it will allow others to dig around if it interests them.
For your second part, there are several options for submitting NGS data. I will recommend submitting your reads (fastq files) in NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra) and mention the SRA number in manuscript. If you use mothur this link could be useful (https://mothur.org/wiki/Make.sra).
Regards
Rumakanta
Thanks a lot for your input Frederic Lepretre, Pasindu Chamikara and Rumakanta Sapkota.
I also got suggestion to use European Nucleotide Archive with submission site https://www.ebi.ac.uk/ena/submit/sra/#home
Just in case - does anybody had an ideas which one is easier/straightforward to use or more suitable for 16S NGS data?
https://submit.ncbi.nlm.nih.gov/subs/sra/
The Sequence Read Archive (SRA) accepts genetic data and the associated quality scores produced by next generation sequencing technologies.
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