Tag: GenBank

GenBank Release 247.0

GenBank release 247.0 (12/19/2021) is now available on the NCBI FTP site. This release has 16.47 trillion bases and 2.59 billion records. 

The current release has 234,557,297 traditional records containing 1,053,275,115,030 base pairs of sequence data. There are also 1,734,664,952 WGS records containing 14,922,033,922,302 base pairs of sequence data, 514,158,576 bulk-oriented TSA records containing 455,870,853,358 base pairs of sequence data, and 109,379,021 bulk-oriented TLS records containing 41,143,480,750 base pairs of sequence data. Continue reading “GenBank Release 247.0”

Join NCBI at PAG XXIX

Join NCBI at PAG XXIX

Introducing the NIH Comparative Genomics Resource (CGR)

NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG XXIX), January 8-12, 2022 in San Diego, California. We’re especially excited to introduce our newest endeavor – the NLM initiative known as the NIH Comparative Genomics Resource (CGR)– a platform we are developing to support comparative analyses of sequenced eukaryotic research organisms. Understanding and supporting the needs of researchers is a fundamental element in the development of CGR and is critical to its future success in supporting a large and diverse collection.

Please join NCBI for the following events to learn more about CGR and how you can inform its development:

Continue reading “Join NCBI at PAG XXIX”

GenBank release 246.0

GenBank release 246.0

GenBank release 246.0 (11/2/2021) is now available on the NCBI FTP site. This release has 16.1 trillion bases and 2.57 billion records.

The current release has 233642893 traditional records containing 1,014,763,752,113 base pairs of sequence data. There are also 1,721,064,101 WGS records containing 14,599,101,574,547 base pairs of sequence data, 508,319,391 bulk-oriented TSA records containing 449,891,016,597 base pairs of sequence data, and 107,569,935 bulk-oriented TLS records containing 40,168,874,815 base pairs of sequence data.

Continue reading “GenBank release 246.0”

Four new options to simplify your SARS-CoV-2 submissions

Four new options to simplify your SARS-CoV-2 submissions

We have recently added several exciting improvements to the SARS-CoV-2 GenBank submission process based on community feedback. To save you time, NCBI completes feature annotation for you, which means SARS-CoV-2 GenBank submission only requires a FASTA file and source metadata. Here are other new features to ease and simplify your submission workflow.

Automatically remove failed sequences from a submission: On the web, a single click lets you opt-in to automatic removal of failed sequences (Figure 1) so that the rest of your sequences can be swiftly accessioned! A report provided after the submission lists your failed sequences and points out potential sequence problems so that you can take a closer look after your error-free sequences are released. This option is also available for submission via FTP.

Need to set up FTP submissions? The NCBI team is here to help. Contact gb-admin@ncbi.nlm.nih.gov.

Figure 1. GenBank submission page showing the option to remove sequences with processing errors.

Continue reading “Four new options to simplify your SARS-CoV-2 submissions”

GenBank release 245.0

GenBank release 245.0 (8/18/2021) is now available on the NCBI FTP site. This release has 15.31 trillion bases and 2.49 billion records.

The current release has 231,982,592 traditional records containing 940,513,260,726 base pairs of sequence data. There are also 1,653,427,055 WGS records containing 13,888,187,863,722 base pairs of sequence data, 498,305,045 bulk-oriented TSA records containing 440,578,422,611 base pairs of sequence data, and 106,995,218 bulk-oriented TLS records containing 39,930,167,315 base pairs of sequence data.

Continue reading “GenBank release 245.0”

GenBank release 244.0

GenBank release 244.0 (6/26/2021) is now available on the NCBI FTP site. This release has 14.78 trillion bases and 2.46 billion records.

The current release has 227,888,889 traditional records containing 866,009,790,959 base pairs of sequence data. There are also 1,632,796,606 WGS records containing 13,442,974,346,437 base pairs of sequence data, 494,641,358 bulk-oriented TSA records containing 436,594,941,165 base pairs of sequence data, and 102,662,929 bulk-oriented TLS records containing 38,198,113,354 base pairs of sequence data. Continue reading “GenBank release 244.0”

GenBank release 243.0

GenBank release 243.0 (5/26/2021) is now available on the NCBI FTP site. This release has 14.03 trillion bases and 2.40 billion records.

The current release has 227,123,201 traditional records containing 832,400,799,511 base pairs of sequence data. There are also 1,590,670,459 WGS records containing 12,732,048,052,023 base pairs of sequence data, 481,154,920 bulk-oriented TSA records containing 425,076,483,459 base pairs of sequence data, and 102,395,753 bulk-oriented TLS records containing 37,998,534,461 base pairs of sequence data. 

Continue reading “GenBank release 243.0”

New class value and qualifier in GenBank release 242.0 accommodate circular RNA molecules

GenBank release 242.0 (2/16/2021) is now available on the NCBI FTP site and through Entrez and BLAST. This release has 13.49 trillion bases and 2.34 billion records.

Growth between releases

During the 57 days between the close dates for GenBank Releases 241.0 and 242.0, the ‘traditional’ portion of GenBank grew by 53,287,389,099 base pairs and by 4,773,649 sequence records. During that same period, 65,699 records were updated. An average of 84,901 ‘traditional’ records were added and/or updated per day.

Between releases 241.0 and 242.0, the WGS component of GenBank grew by 439,874,781,594 base pairs and by 45,942,354 sequence records. During the same period, the TSA component of GenBank grew by 15,398,434,562 base pairs and by 16,753,622 Sequence records. Finally, the TLS component of GenBank grew by 597,613,549 base pairs and by 2,091,409 sequence records.

Continue reading “New class value and qualifier in GenBank release 242.0 accommodate circular RNA molecules”

GenBank release 241.0

GenBank release 241.0 (12/21/2020) is now available on the NCBI FTP site. This release has 12.98 trillion bases and 2.27 billion records.

The current release has 221,467,827 traditional records containing 723,003,822,007 base pairs of sequence data. There are also 1,517,995,689 WGS records containing 11,830,842,428,018 base pairs of sequence data, 446,397,378 bulk-oriented TSA records containing 392,206,975,386 base pairs of sequence data, and 88,039,152 bulk-oriented TLS records containing 33,036,509,446 base pairs of sequence data. Continue reading “GenBank release 241.0”

GenBank 240.0 is available and surpasses 10 trillion basepairs!

GenBank release 240.0 (10/28/2020) is now available on the NCBI FTP site. This release has 10.33 trillion bases and 2.17 billion records.

The current release has 219,055,207 traditional records containing 698,688,094,046 base pairs of sequence data. There are also 1,432,874,252 WGS records containing 9,215,815,569,509 base pairs of sequence data, 435,968,379 bulk-oriented TSA records containing 382,996,662,270 base pairs of sequence data, and 78,177,358 bulk-oriented TLS records containing 28,814,798,868 base pairs of sequence data.

Growth between releases

During the 71 days between the close dates for GenBank Releases 239.0 and 240.0, the ‘traditional’ portion of GenBank grew by 44,631,024,497 basepairs and by 412,969 sequence records. During that same period, 94,006 records were updated. An average of 7,140 ‘traditional’ records were added and/or updated per day.

Between releases 239.0 and 240.0, the WGS component of GenBank grew by 374,166,158,857 basepairs and by 24,751,365 sequence records. The TSA component of GenBank grew by 16,027,711,110 basepairs and by 18,443,812 sequence records. The TLS component of GenBank grew by 989,739,370 basepairs and by 2,495,201 sequence records.

The total number of sequence data files increased by 107 with this release. The divisions are as follows:

  • BCT: 22 new files, now a total of 512
  • CON: 1 new file, now a total of 218
  • INV: 2 new files, now a total of 97
  • PAT: 1 new file, now a total of 213
  • PLN: 47 new files, now a total of 594
  • PRI: 10 new files, now a total of 45
  • ROD: 15 new files, now a total of 56
  • VRL: 5 new files, now a total of 44
  • VRT: 4 new files, now a total of 214

Delivery of GenBank 240.0 was delayed by two weeks

A power surge at the NCBI data center and subsequent downtime for a critical disk storage system led to a nearly two-week delay in the delivery of the data files for GenBank 240.0. There were no data losses, and public-facing systems remained available. However, between the direct impacts of the outage and subsequent efforts to resume processing pipelines, the GenBank release timeline was significantly pushed back. Our apologies for the delay!

Upcoming Changes

New /ncRNA_class value : circRNA

  • The allowed values for the /ncRNA_class qualifier have been extended to include “circRNA”, for circular RNA molecules. This change will not appear until (or after) GenBank Release 242.0 in February 2021.

New /circular_RNA qualifier

  • Complementing the new “circRNA” ncRNA class, a new qualifier will be introduced in (or after) GenBank Release 242.0 in February 2021.

Additional Information

For downloading purposes, please keep in mind that the uncompressed GenBank Release 240.0 sequence data flatfiles require roughly 1,524 GB. The ASN.1 data files require approximately 958 GB.

More information about GenBank release 240.0 is available in the release notes, as well as in the README files in the genbank and ASN.1 (ncbi-asn1) directories on FTP.