GenBank Release 229.0 Available : December 20 2018 : 6:12pm

[Cavanaugh, Mark (NIH/NLM/NCBI) [E]]

Greetings GenBank Users,

GenBank Release 229.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):

Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 229.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 229.0

Close-of-data for GenBank 229.0 occurred on 12/15/2018. Uncompressed,
the Release 229.0 flatfiles require roughly 934 GB (sequence files only).
The ASN.1 data require approximately 760 GB.

Recent statistics for 'traditional' sequences (including non-bulk-oriented
TSA, and excluding WGS, bulk-oriented TSA, TLS, and the CON-division):

Release Date Base Pairs Entries

228 Oct 2018 279668290132 209656636
229 Dec 2018 285688542186 211281415

Recent statistics for WGS sequencing projects:

Release Date Base Pairs Entries

228 Oct 2018 3444172142207 722438528
229 Dec 2018 3656719423096 773773190

Recent statistics for bulk-oriented TSA sequencing projects:

Release Date Base Pairs Entries

228 Oct 2018 235875573598 259927414
229 Dec 2018 248592892188 274845473

Recent statistics for bulk-oriented TLS sequencing projects:

Release Date Base Pairs Entries

228 Oct 2018 8435112913 20752288
229 Dec 2018 8511829281 20924588

During the 61 days between the close dates for GenBank Releases 228.0
and 229.0, the 'traditional' portion of GenBank grew by 6,020,252,054
basepairs and 1,624,779 sequence records. During that same period,
96,194 records were updated. An average of 28,213 'traditional' records
were added and/or updated per day.

Between releases 228.0 and 229.0, the WGS component of GenBank grew by
212,547,280,889 basepairs and by 51,334,662 sequence records.

Between releases 228.0 and 229.0, the TSA component of GenBank grew by
12,717,318,590 basepairs and by 14,918,059 sequence records.

Between releases 228.0 and 229.0, the TLS component of GenBank grew by
76,716,368 basepairs and by 172,300 sequence records.

For additional release information, see the README files in either of
the directories mentioned above, and the release notes (gbrel.txt) in
the genbank directory. Sections 1.3 and 1.4 of the release notes
(Changes in Release 229.0 and Upcoming Changes) have been appended
below for your convenience.

* * * Important Notice * * *

Section 1.4.1 of the GenBank release notes describes future accession
format changes for traditional nucleotide sequences, WGS/TSA/TLS
sequences, and for protein sequences. These important changes are likely
to be of interest to many GenBank users, and we encourage a review of
the section.

Release 229.0 data, and subsequent updates, are available now via
NCBI's Entrez and Blast services.

As a general guideline, we suggest first transferring the GenBank
release notes (gbrel.txt) whenever a release is being obtained. Check
to make sure that the date and release number in the header of the
release notes are current (eg: December 15 2018, 229.0). If they are
not, interrupt the remaining transfers and then request assistance from
the NCBI Service Desk.

A comprehensive check of the headers of all release files after your
transfers are complete is also suggested. Here's how one might go about
this on a Unix or Linux platform, using csh/tcsh :

set files = `ls gb*.*`
foreach i ($files)
head -10 $i | grep Release
end

Or, if the files are compressed, perhaps:

gzcat $i | head -10 | grep Release

If you encounter problems while ftp'ing or uncompressing Release
229.0, please send email outlining your difficulties to:

in...@ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky
GenBank
NCBI/NLM/NIH/HHS


1.3 Important Changes in Release 229.0

1.3.1 Organizational changes

The total number of sequence data files increased by 55 with this release:

- the BCT division is now composed of 566 files (+24)
- the CON division is now composed of 375 files (+3)
- the ENV division is now composed of 105 files (+2)
- the EST division is now composed of 489 files (+3)
- the INV division is now composed of 117 files (+5)
- the PAT division is now composed of 347 files (+7)
- the PLN division is now composed of 241 files (+9)
- the VRL division is now composed of 59 files (+1)
- the VRT division is now composed of 95 files (+1)

1.3.2 GSS File Header Problem

GSS sequences at GenBank are maintained in two different systems, depending
on their origin, and the dumps from those systems occur in parallel. Because
the second dump (for example) has no prior knowledge of exactly how many GSS
files will be dumped by the first, it does not know how to number its own
output files.

There is thus a discrepancy between the filenames and file headers for 130
of the GSS flatfiles in Release 229.0. Consider gbgss179.seq :

GBGSS1.SEQ Genetic Sequence Data Bank
December 15 2018

NCBI-GenBank Flat File Release 229.0

GSS Sequences (Part 1)

87375 loci, 64103840 bases, from 87375 reported sequences

Here, the filename and part number in the header is "1", though the file
has been renamed as "179" based on the number of files dumped from the other
system. Files gbgss179.seq.gz through gbgss308.seq.gz are affected. We hope
to resolve this discrepancy at some point, but the priority is certainly
much lower than many other tasks.

1.4 Upcoming Changes

1.4.1 Changes to nucleotide and protein accession formats

The accession format used for Whole Genome Shotgun (WGS), Transcriptome
Shotgun Assembly (TSA), and Targeted Locus Study (TLS) sequencing projects
consists of a four-letter Project Code prefix, a two-digit Assembly-Version
number, followed by 6, 7, or 8 digits (depending on the number of sequences
in the project).

By the end of 2018 the INSDC members plan to expand this format, using
a six-letter Project Code prefix, two-digit Assembly-Version number, followed
by 7, 8, or 9 digits. An example of such an accession is AAAAAA020000001 .

Non-WGS/TLS/TSA nucleotide sequences currently make use of a "2+6"
accession format, consisting of a two-letter prefix followed by six digits.
This format will be expanded to make use of eight digits, allowing accession
ranges that have been exhausted (eg: JG000001-JG999999) to be "re-opened"
(eg: JG00000001-JG99999999).

Protein sequences currently make use of a "3+5" accession format, consisting
of a three-letter prefix followed by five digits. This format will be expanded
to make use of seven digits, allowing exhausted protein accession ranges such
as EZZ00001-EZZ99999 to be re-opened as EZZ0000001-EZZ9999999.

The earliest date on which these new accessions could begin to appear for
GenBank sequences is December 21st 2018.