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.
> -----Original Message-----
> From: Cavanaugh, Mark (NIH/NLM/NCBI) [E]
> Sent: Thursday, August 17, 2017 11:34 PM
> To: 'genbankb from net.bio.net' (genbankb from net.bio.net)
> <genbankb from net.bio.net>
> Subject: GenBank Release 221.0 Available : August 17 2017
>> 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:
>>info from 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.
