GenBank

Submitting HTG Sequences

If you are new to HTG submissions please start here.

The HTG division contains unfinished DNA sequences generated by the high-throughput sequencing centers using traditional clone-based Sanger sequencing.

Draft genomes sequenced using non-clone based whole genome shotgun sequencing are not appropriate for HTG, these should be submitted as a WGS submission as described at www.ncbi.nlm.nih.gov/Genbank/wgs.html. NextGen sequences and should not be submitted to HTG instead these should be submitted to the Sequence Read Archive. For general submission information, please start here.

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, 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 NCBI should email htgs-admin@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. PLEASE NOTE most nucleotide sequence submissions to NCBI do NOT use an FTP account. The instructions here are specific to high-throughput genomic sequences (HTG).

Submission Tools

There are currently two ways to create HTG records:

1. The Sequin program Sequin will soon be retired and if you are using Sequin for HTG submissions, you should switch to tbl2asn. 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 tbl2asn tool tbl2asn is a command-line program that has replaced the deprecated program fa2htgs. tbl2asn 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). tbl2asn then generates the ASN.1 file for submission. tbl2asn can be incorporated into scripts to facilitate expedient processing of records.