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Submitting HTGs

The submission process for HTGs is quite different from that for other direct submissions. The goal of the process is to make new and updated sequences available to the public in a timely fashion. Thus, the NCBI will perform only very basic validation checks of HTGs, and submitters must check their records carefully before submission. Furthermore, because sequences will be released to the public as soon as processing is finished, it is presently not the standard procedure to indicate a "hold until published" (HUP) date on which they should be released. If a HUP date is necessary, the submitter should please contact the database staff about submitting through an alternate route.

Sequencing centers that will be submitting HTGs to the NCBI should contact the NCBI (info@ncbi.nlm.nih.gov) to establish an FTP account. Prepared records should be transferred to this site, where they will be retrieved daily by the NCBI staff. These records should not be emailed to the NCBI. Submitted HTG sequences must be written in ASN.1 format.

There are currently four ways to create HTG records:

1. The Sequin program
   Sequin contains a setting that allows genome centers to prepare HTG submissions. Sequin reads in a FASTA sequence file (or an Ace Contig file with Phrap sequence quality values) and a Sequin submission template file (to get contact and citation information). Users then enter additional information into a Sequin form, the same information that they would enter at the command line in fa2htgs (see below). Sequin generates the ASN.1 file for submission.

2. The fa2htgs tool
   fa2htgs reads in a FASTA sequence file (or an Ace Contig file with Phrap sequence quality values), a Sequin submission template file (to get contact and citation information), and a series of command-line arguments (to get additional information). fa2htgs then generates the ASN.1 file for submission. fa2htgs can be incorporated into scripts to facilitate expedient processing of records. It can be used at the command line or interactively within Sequin (see above).

3. The tbl2asn tool
   tbl2asn is a newer command-line program that is replacing fa2htgs. It also generates the ASN.1 file for submission from a FASTA sequence file (or an Ace Contig file with Phrap sequence quality values), a Sequin submission template file (to get contact and citation information), and a series of command-line arguments (to get additional information). We recommend that submitters use this program rather than fa2htgs.

4. Your own tool
   Some genome centers have written their own tool (sometimes with help and suggestions from software developers at NCBI) that will produce HTG submissions. These are a special type of ASN.1 formatted records, and centers that want to generate such submissions are invited to look into the NCBI toolkit and to consult with NCBI (info@ncbi.nlm.nih.gov) to ensure that correct ASN.1 is generated.

Revised: February 13, 2008.