HTG FAQs

Please send any additional questions to htg-admin@ncbi.nlm.nih.gov, and we will include them if they are appropriate.

• What Phase should my HTG submission be?
• What do the different KEYWORDS mean?
• Where do I send an HTG update?
• How do I submit HTG sequences?

What Phase should my HTG submission be?

If the HTG record is unfinished, it should be designated Phase 1 or Phase 2. Phase 1 indicates an unfinished sequence containing gaps, in which the order and relative orientation of the pieces are not known. Phase 2 is also an unfinished sequence, but the order and orientation of the pieces are known, however, the length of the gaps between these pieces may or may not be known. By definition, an unfinished sequence of only one piece is Phase 2. Phase 3 submissions are one contiguous piece of DNA of finished quality.

What do the different KEYWORDS mean?

• HTGS_DRAFT

  Clones that are sequenced to draft status. These should be, on average over all draft depositions, at least 4X coverage (but can be more) and are Phase 1 or Phase 2.

• HTGS_FULLTOP

  An HTGS_DRAFT clone where all shotgun reads are done. At this point, the project is ready to hand off to finishers. A deposition should be made at this stage. Note that the precise coverage will vary depending on center operating procedure, but usually the coverage is between 6X and 10X. These projects are almost always ordered and oriented (Phase 2).

• HTGS_PREFIN

  After the HTGS_FULLTOP stage, when the clone has undergone 2 rounds of prefinishing (two iterative computational determinations of low coverage/low quality regions and addition of directed sequencing reads, including primer walks, covering those areas followed by re-assembly, in an attempt to improve contiguity and quality).

• HTGS_IMPROVED

  After the HTGS_FULLTOP stage, when one or more regions of the BAC are of finished quality.

• HTGS_ACTIVEFIN

  The fulltop project has been passed to the finishing team. Often this happens very rapidly after HTGS_fulltop is reached.

• HTGS_ENRICHED

  The BAC assembly is enriched by inclusion of both BAC generated reads and overlapping WGS reads.

• HTGS_POOLED_MULTICLONE

  The assembly consists of reads from multiple BAC clone reads that have not yet been deconvoluted from an array of pooled clones. The keyword is valid for Phase 0, 1, and 2 HTGS records, but not Phase 3. The clone names must be present in the /clone qualifier, separated by a semi-colon.

• HTGS_POOLED_CLONE

  The assembly consists of a specific BAC clone's reads that were deconvoluted from an array of pooled clones; contains overlapping reads from WGS sequencing if used in conjunction with HTGS_ENRICHED.

• HTGS_CANCELLED

  Sequencing of the clone has stopped, and this clone will not be finished.

• HTGS_LIMITED_ORDER

   A clone in which the order and orientation is known for some of the contigs, but not all of them. This can be used for Phase 1 clones.

• GAP_CLOSURE

  Used for non-HTG records whose sequences close gaps in HTG records

• PCR_CORRECTION

  Used for non-HTG records that are PCR sequences of genomic DNA that were generated to correct small errors in HTG or other sequences of a genome assembly.

Where do I send an HTG update?

Existing users for the HTG submission system can continue to update their records through the HTG system until January 2021. After that time all updates should be sent per these instructions https://www.ncbi.nlm.nih.gov/genbank/update/.
All other users should also follow the instructions at https://www.ncbi.nlm.nih.gov/genbank/update/.