GenBank Release 221.0 Available : August 17 2017

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

Greetings GenBank Users,

GenBank Release 221.0 is now available via FTP from the National Center
for Biotechnology Information (NCBI):

Ftp Site Directory Contents
---------------- --------- ---------------------------------------
ftp.ncbi.nih.gov genbank GenBank Release 221.0 flatfiles
ncbi-asn1 ASN.1 data used to create Release 221.0

Close-of-data for GenBank 221.0 occurred on 08/13/2017. Uncompressed,
the Release 221.0 flatfiles require roughly 841 GB (sequence files only).
The ASN.1 data require approximately 698 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

220 Jun 2017 234997362623 201663568
221 Aug 2017 240343378258 203180606

Recent statistics for WGS sequencing projects:

Release Date Base Pairs Entries

220 Jun 2017 2164683993369 487891767
221 Aug 2017 2242294609510 499965722

Recent statistics for bulk-oriented TSA sequencing projects:

Release Date Base Pairs Entries

220 Jun 2017 158112969073 176812130
221 Aug 2017 167045663417 186777106

Recent statistics for bulk-oriented TLS sequencing projects:

Release Date Base Pairs Entries

220 Jun 2017 824191338 1628475
221 Aug 2017 824191338 1628475 (unchanged)

During the 56 days between the close dates for GenBank Releases 220.0
and 221.0, the 'traditional' portion of GenBank grew by 5,346,015,635
basepairs and by 1,517,038 785,684 sequence records. During that same period,
180,064 records were updated. An average of 30,305 'traditional' records
were added and/or updated per day.

Between releases 220.0 and 221.0, the WGS component of GenBank grew by
77,610,616,141 basepairs and by 12,073,955 sequence records.

Between releases 220.0 and 221.0, the TSA component of GenBank grew by
8,932,694,344 basepairs and by 9,964,976 sequence records.

Between releases 220.0 and 221.0, the TLS component of GenBank was unchanged.

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 221.0 and Upcoming Changes) have been appended
below for your convenience.

Release 221.0 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: August 15 2017, 221.0). 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
221.0, 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 221.0

1.3.1 Organizational changes

The total number of sequence data files increased by 45 with this release:

- the BCT division is now composed of 391 files (+21)
- the CON division is now composed of 359 files (-4)
- the INV division is now composed of 155 files (+1)
- the PAT division is now composed of 294 files (+3)
- the PLN division is now composed of 150 files (+2)
- the PRI division is now composed of 57 files (+1)
- the TSA division is now composed of 234 files (+4)
- the VRL division is now composed of 50 files (+1)
- the VRT division is now composed of 80 files (+16)

The decrease in the number of CON files is due to the removal of GI
sequence identifiers on the VERSION and COMMENT lines of the GenBank
flatfile format.

1.3.3 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 221.0. Consider gbgss175.seq :

GBGSS1.SEQ Genetic Sequence Data Bank
August 15 2017

NCBI-GenBank Flat File Release 221.0

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 "175" based on the number of files dumped from the other
system. Files gbgss175.seq.gz through gbgss304.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 No changes impacting GenBank Release content are currently planned.

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

Correction:

> During the 56 days between the close dates for GenBank Releases 220.0
> and 221.0, the 'traditional' portion of GenBank grew by 5,346,015,635
> basepairs and by 1,517,038 785,684 sequence records. During that same period,
> 180,064 records were updated. An average of 30,305 'traditional' records
> were added and/or updated per day.

The 785,684 statistic is from GenBank 220.0 . The paragraph should read:

During the 56 days between the close dates for GenBank Releases 220.0
and 221.0, the 'traditional' portion of GenBank grew by 5,346,015,635

basepairs and by 1,517,038 sequence records. During that same period,

180,064 records were updated. An average of 30,305 'traditional' records
were added and/or updated per day.