SEA-PHAGES | GenBank Submissions

Link to this post \| posted 11 May, 2023 18:18
scaruso	Hello, I am at one of the schools that not only sends phage genomes to PITT for submission, but occassionally submits to GenBank directly when we work on different species. We do so by emailing the submission file in right from DNAM with the appropriate information. Recently I received a note that there is a format change (see below) and I now wonder if requires a change I am unsure how to make. If anyone can share any updates on this, I would be grateful. Thanks! Steve You are receiving this message to inform you that NCBI has replaced tbl2asn with the newer more powerful command line program table2asn. table2asn performs the validations that occur during processing of submissions and has some additional functionality so we recommend that you use it instead of tbl2asn for future annotated genome submissions. We will process this tbl2asn submission. DO NOT resubmit it. You will be contacted regarding its processing in a separate message, and you can complete any necessary changes to this submission as usual. However, for future submissions, we encourage you to use the newer command line program table2asn to generate the appropriate .sqn file for submission. Information about table2asn can be found at: https://www.ncbi.nlm.nih.gov/genbank/table2asn/ The values of a few arguments have changed compared to tbl2asn. In particular: Old New Purpose —————————————————————– - -help to get a summary of the command line arguments -p -indir to use all the .fsa files in the specified directory as input -r -outdir to deposit the output files in the specified directory -Z <file> -Z to run the discrepancy report -a r10k -gaps-min 10 to convert runs of 10 or more Ns to gaps of estimated size

Link to this post | posted 11 May, 2023 18:18

Hello,

I am at one of the schools that not only sends phage genomes to PITT for submission, but occassionally submits to GenBank directly when we work on different species. We do so by emailing the submission file in right from DNAM with the appropriate information. Recently I received a note that there is a format change (see below) and I now wonder if requires a change I am unsure how to make.

If anyone can share any updates on this, I would be grateful.

Thanks!

Steve
You are receiving this message to inform you that NCBI has replaced tbl2asn with the newer more powerful command line program table2asn.
table2asn performs the validations that occur during processing of submissions and has some additional functionality so we recommend that you use it instead of tbl2asn for future annotated genome submissions.

We will process this tbl2asn submission. DO NOT resubmit it.
You will be contacted regarding its processing in a separate message, and you can complete any necessary changes to this submission as usual.

However, for future submissions, we encourage you to use the newer command line program table2asn to generate the appropriate .sqn file for submission.

Information about table2asn can be found at:

https://www.ncbi.nlm.nih.gov/genbank/table2asn/

The values of a few arguments have changed compared to tbl2asn.
In particular:

Old New Purpose
—————————————————————–
- -help to get a summary of the command line arguments
-p -indir to use all the .fsa files in the specified directory as input
-r -outdir to deposit the output files in the specified directory
-Z <file> -Z to run the discrepancy report
-a r10k -gaps-min 10 to convert runs of 10 or more Ns to gaps of estimated size

Link to this post \| posted 11 May, 2023 19:09
debbie	Steve, If you are using DNA maser to submit genomes, you can ignore this. We are in compliance. debbie

Link to this post \| posted 11 May, 2023 19:12
scaruso	Debbie, OK. Thanks! I was worried about a summer isolated Bt phage and that I was getting a warning. I will keep on keeping on if we do anymore. Though we annotate Strep in the summer, too. Thanks! Steve

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