#INSDC
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bffo.bsky.social
From the @ebi.embl.org team in @narjournal.bsky.social #NARDatabaseIssue | The European Nucleotide Archive in 2026 | #Bioinformatics #Database #WebServer #OpenScience
#ENA #INSDC #Proteomics #Genomics #OpenData #Biocuration | 🧬🖥️🧪🔓
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academic.oup.com/nar/advance-...
The European Nucleotide Archive in 2026
Abstract. The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), hosted at EMBL’s European Bioinformatics Institute, is an open resource that su
academic.oup.com
November 6, 2026 at 5:54 PM
tylerbarnumphd.bsky.social
The standard is that all MAGs should be submitted to an INSDC repository. The genomes aren't really "available" because a lot of effort is required to find & use individual repositories. See:

www.ncbi.nlm.nih.gov/genbank/wgsfaq/#metagen
doi.org/10.1038/nbt.3893
doi.org/10.1093/bioadv/vbaf280
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea - Nature Biotechnology
Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed.
doi.org
October 16, 2026 at 2:05 PM
nextflow.io
📤 Submitting data to public archives is a notorious bottleneck. Ekaterina Sakharova (@ebi.embl.org) presented @nf-co.re /seqsubmit, a Nextflow pipeline that automates submitting reads, assemblies & MAGs to ENA, calculating any missing stats. hubs.la/Q04zpWTq0 #NextflowSummit
nf-core/seqsubmit: pipeline for automated data submission to INSDC resources – Ekaterina Sakharova | Nextflow Summit 2026
Join us at Nextflow Summit 2026 for the latest developments and innovations from the Nextflow world.
hubs.la
October 13, 2026 at 1:50 PM
bananabenana.bsky.social
Shoutout to NCBI for the amazing tree of life swiss army knife that is the Genbank cinematic universe.

Website is intuitive + powerful, API is useful for large-scale im/exports making big genomics feasible. INSDC member enduring mirrored copies on different servers.

Legendary institution
October 7, 2026 at 12:35 PM
bede.im
This is a big deal for virus data sharing. Submitters can now upload raw reads, immediately share them with collaborators, and let Pathoplexus take care of the INSDC submission process on their behalf…
pathoplexus.org Pathoplexus @pathoplexus.org · Sep 22
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences!

Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.

📰 Read more: pathoplexus.org/news/2026-09...
AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.
September 23, 2026 at 1:06 PM
nextflow.io
Ekaterina Sakharova (@ebi.embl.org) → @nf-co.re/seqsubmit: pipeline for automated data submission to INSDC resources

summit.nextflow.io/2026/virtual...
nf-core/seqsubmit: pipeline for automated data submission to INSDC resources – Ekaterina Sakharova | Nextflow Summit 2026
Join us at Nextflow Summit 2026 for the latest developments and innovations from the Nextflow world.
summit.nextflow.io
September 23, 2026 at 2:59 PM
pathoplexus.org
2/ ⚙️ How it works: raw reads follow all the same policies as consensus sequences - your chosen Data Use Terms apply to both, and raw reads are openly downloadable as soon as processing completes.

Pathoplexus handles INSDC submission for you, just like today.
Screenshot of the submission page showing the section to upload raw-reads - with a description and link to the documentation on the left, and a place to upload folders and files on the right.
September 22, 2026 at 8:06 PM
bffo.bsky.social
From @colmanoc.bsky.social and colleagues in #OUP 's #DATABASE journal | The INSDC specifications--foundations for a #FAIR and global INSDC | #Bioinformatics #OpenScience #OpenData #INSDC #GenBank @enasequence.bsky.social #DDBJ #NCBI CC/ @ebi.embl.org | 🧬🖥️🧪🔓
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academic.oup.com/database/art...
The INSDC specifications—foundations for a FAIR and global INSDC
Abstract. Members of the International Nucleotide Sequence Database Collaboration (INSDC; https://www.insdc.org/) collect, exchange, and preserve comprehen
academic.oup.com
September 8, 2026 at 12:40 PM
rmwaterhouse.bsky.social
Great to see both ERGA @ergabiodiv.bsky.social and #arthropods featuring at #Quest4Orthologues in #Lausanne today! #biodiversity #genomics Talk from Odile Lecompte, University of Strasbourg #Myriapoda - only 4 of the publicly available #genomes have annotations at INSDC databases
August 29, 2026 at 9:22 AM
ergabiodiv.bsky.social
💡 #KnowledgeHighlight | Take a quick tour of the European Nucleotide Archive @enasequence.bsky.social 🧬🖱️
🔗 ebi.ac.uk/training/onl...

Explore more open-access training materials in the ERGA #KnowledgeHub ➡️ knowledge.erga-biodiversity.eu

#IT #Infrastructure #INSDC @embl.org @ebi.embl.org
European Nucleotide Archive - Quick tour
European Nucleotide Archive - Quick tour
ebi.ac.uk
June 10, 2025 at 7:38 AM
rchristo.bsky.social
Are GenBank sequences deposited into INSDC? Or do we need to start moving stuff over there?
March 2, 2025 at 2:01 PM
colmanoc.bsky.social
A milestone in INSDC history, and these specifications help set out a framework for widening participation in this gloabl collaboration of nearly 40 years.
March 18, 2026 at 3:40 PM
colmanoc.bsky.social
The INSDC has today launched its minimal specifcations. This has been a huge amount of work over several years involving European Nucleotide Archive staff both past and present, but also our colleagues NCBI and DDBJ.
ebi.embl.org EMBL-EBI @ebi.embl.org · Mar 18
Life science research depends on global access to sequencing data but this only works when everyone speaks the same technical language.

Find out how the INSDC has updated its specifications to simplify data submission for better synchronisation across its partners.

www.ebi.ac.uk/about/news/a...
New specifications for submitting nucleotide sequence data
New INSDC standards support simpler submissions and improve synchronisation of global genome sequence data.
www.ebi.ac.uk
March 18, 2026 at 3:40 PM
dannyjpark.bsky.social
Yes, all of nih.gov going down is bad of course, regardless of whether it’s malicious or a technical oops that will get fixed eventually (tldr.nettime.org/@ww/11408997...), but I do encourage everyone to learn about the federated nature of the INSDC (including Genbank and PubMed)
ww (@ww@tldr.nettime.org)
Attached: 2 images So, three nameservers out of seven for the pubmed.ncbi.nlm.nih.gov are broken. If you try to look at the web site, you stand a 3/7 chance of encountering something that is broken. ...
tldr.nettime.org
March 2, 2025 at 1:55 PM
dominiquechaput.bsky.social
Agreed, sequence databases appear robust thanks to the INSDC - a testament to scientists collaborating globally to share and preserve data. But the sequence search tool on ENA, at least, appears to rely on ncbi BLAST so we may need to consider local implementations if we lose ncbi.
March 2, 2025 at 2:42 PM
dominiquechaput.bsky.social
No need for you to move anything, data from all INSDC members is mirrored across the consortium. If you search, e.g. ENA, you will find sequences originally deposited in GenBank. Quite a remarkable system, a testament to what can be done when scientists collaborate to share and preserve data.
March 2, 2025 at 2:24 PM
bacdive.bsky.social
🧬 #BacDive is also taking a long-awaited leap into the world of genomics with the debut of a genome browser 🔎🖥️.

For the first time, BacDive now displays genomic information. The genome browser feature lists and visualizes #Bakta annotations of #INSDC genome assemblies.
The new genome browser tool.
December 19, 2025 at 12:11 PM
hollywoodindc.bsky.social
Worth a watch. youtube.com/shorts/iNSdc...
I just got out of Nicolas Maduro’s court hearing in New York City .
YouTube video by Brian Entin
youtube.com
January 5, 2026 at 6:53 PM
usadellab.bsky.social
Have a look here www.plabipd.de/plant_genome... where we try to keep track of sequenced and available genomes (mostly INSDC).
March 21, 2024 at 10:34 AM
linsalrob.bsky.social
"anything [in the INSDC] from >10 years ago is such a small blip, it would take you longer to find it and delete it than its worth, you might as well leave it be".

Sequence data production is exponential!

Dr Joanna McEntyre, EMBL-EBI

#ABACBS2025
November 24, 2025 at 11:23 PM
felipers.bsky.social
"The DNA banks representing Japan, Europe, and the USA are respectively called the DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank; all three are part of the INSDC where they share data and collaborate to maintain a global database of DNA sequences".
March 2, 2025 at 6:33 PM
felipers.bsky.social
Principalmente! Os três juntos formam o INSDC (International Nucleotide Sequence Database Collaboration).

Países inteligentes (e com dinheiro) não dependem de dados que eles não controlam!
March 2, 2025 at 6:32 PM
caseybergman.bsky.social
The founders of INSDC set up international mirroring in part to prevent any one government from trying to control/privitize the information. Very prescient decision.
February 4, 2025 at 12:55 AM
profcolinbean.bsky.social
Sequence data submitted to GenBank and the SRA will need to include information about location and date and time of sample collection.
ncbiinsights.ncbi.nlm.nih.gov/2023/05/01/s...
Coming Soon! Including Sample Location and Collection Date and Time for Sequences Submitted to GenBank and SRA - NCBI Insights
As previously announced, in collaboration with our partners at the International Nucleotide Sequence Database Collaboration (INSDC), we will begin to systematically gather ‘location of collection’ and...
ncbiinsights.ncbi.nlm.nih.gov
December 13, 2024 at 1:17 PM