Tag: submissions

INSDC Statement on SARS-CoV-2 sequence data sharing during COVID-19

The National Library of Medicine and its partners in the International Nucleotide Database Collaboration (INSDC) have joined together to issue a statement encouraging the scientific community to submit their SARS-CoV-2 sequences to INSDC databases. The databases offer broad open access and integrated data, literature and tools – features that we believe are critical as the research community works together to understand and combat COVID-19.  Read the full statement below.


The databases of the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) capture, organize, preserve and present nucleotide sequence data as part of the open scientific record. INSDC member institutions – the EMBL European Bioinformatics Institute (EMBL-EBI), the NIG DNA Data Bank of Japan (NIG-DDBJ) and the National Library of Medicine’s National Center for Biotechnology Information at NIH (NCBI) – are committed to the continued delivery of this critical element of scientific infrastructure.

The global COVID-19 crisis has brought an urgent need for the rapid open sharing of data relating to the outbreak. Most importantly, access to sequence data from the SARS-CoV-2 viral genome is essential for our understanding of the biology and spread of COVID-19. To aid in that effort, all three INSDC members have prioritized processing of SARS-CoV-2 sequence data and have streamlined the submission process.

Availability of data through INSDC databases provides:

    • Rapid open access – INSDC quickly makes submitted data freely available to everyone, without restrictions on reuse
    • Linkage of raw sequence read data to genome assemblies, providing researchers with the ability to validate the integrity of assemblies and investigate asserted mutations and changes in genome sequences
    • Integration of SARS-CoV-2 sequences with entirety of INSDC data, including related coronaviruses genome sequences, enabling comparison across species
    • Linkage of sequences to the published literature
    • Tools – INSDC partners provide integrated data analysis tools, such as BLAST, enhancing the discovery process

In support of the global response to the COVID-19 crisis, the INSDC calls upon the research community to:

    • Submit raw SARS-CoV-2 data to the databases of the INSDC
    • Submit consensus/assembled SARS-CoV-2 data to the databases of the INSDC
    • Provide information relating to the sequenced isolate or sample as part of the sequence submission; minimally the time and place of isolation/sampling and an isolate/sample identifier should be provided to maximize the value of the sequences.
    • In cases where scientists have already established submissions to other databases, these submissions should continue in parallel to the INSDC submission

The integration of INSDC databases with the global bioinformatics data infrastructure, including tools, secondary databases, compute capacity and curation processes, assures the rapid dissemination of data and drives its maximal impact.

In addition to these fundamental roles of INSDC member institutions in the sharing of viral sequence data, each institution has rapidly established COVID-19-specific programs and resources: the European COVID-19 Data Platform from EMBL-EBI, the DDBJ’s Research Data Resources on New Coronavirus and the NCBI SARS-CoV-2 Resources. These resources both demonstrate the connectedness of INSDC databases to broader bioinformatics initiatives and serve to add immediate value to COVID-19 research.

Guy Cochrane (EMBL-EBI), Ilene Karsch-Mizrachi (NCBI-NLM-NIH), & Masanori Arita (DDBJ) on behalf of the International Nucleotide Sequence Database Collaboration

Dengue virus submission improvements now live!

When there is an outbreak of dengue fever in the world, it’s critical that viral genomic sequence data be submitted by researchers and made available to analyze as soon as possible.  You can now submit Dengue virus sequences to GenBank using a new workflow (Figure 1) in the Submission Portal designed to help make these data available as soon as possible.  The streamlined process, similar to the one described in a previous post for animal mitochondrial COX1 sequences, has an improved interface, enhanced validation, and automatic annotation that saves you time and effort.

Dengue_sub

Figure 1. The Submission Portal pages for targeted sequence submission workflows. Top panel. The new submission page for entering the workflow. Bottom panel. Submission Portal page with the Dengue virus submission option selected (boxed in red).  The service has options for other targeted submissions including mitochondrial COX1 from multicellular animals (metazoa), ribosomal RNA (rRNA), rRNA-ITS, Influenza virus, and Norovirus sequences.

This update is part of a larger and ongoing effort to consolidate GenBank submissions in a central location.  In addition to Dengue virus data, you can also submit Influenza A, B, C and Norovirus sequences as well as other targeted sequences including mitochondrial COX1 genes from multicellular animals (metazoa), ribosomal RNA (rRNA), and rRNA-ITS through the options on the Submission Portal.  You should submit other types of sequence data including other virus sequences to GenBank using BankIt or tbl2ASN.

You can use the search feature on the Submission Portal to find the appropriate submission tool for your data.

Mitochondrial COX1 submission improvements now live in submission portal!

GenBank submitters, you can now submit mitochondrial COX1 (cytochrome oxidase subunit I; COI) sequence data from multicellular animals (metazoa) using a new workflow (Figure 1) with an improved interface, enhanced validation, and automatic COX1 CDS feature annotation.  Once you have submitted mitochondrial COX1 data using this tool, you’ll have a single, helpful page to reference your submission information: accession number(s), COX1 submission status, relevant files and more. Plus, you can also fix any errors from this page.

COX1_Submission2
Figure 1. Submission Portal page with the mitochondrial COX1 submission option selected (boxed in red).  The service has options for other targeted submissions including ribosomal RNA (rRNA), rRNA-ITS, Influenza virus, and Norovirus sequences.

Continue reading “Mitochondrial COX1 submission improvements now live in submission portal!”

Feature propagation in BankIt: easily annotate many sequences at once for GenBank submission

Do you need a quick way to annotate features on a similar set of sequences for your GenBank submission? You can now submit sequences from the same region or gene in an alignment format in BankIt and use the new ‘Feature propagation option’ (Figure 1) to apply features from a single sequence to other aligned sequences. You simply annotate one sequence and then copy that annotation across all the sequences in your submission.

Here’s how you can propagate features in three easy steps:

  1. Provide nucleotide sequences in an alignment format.
  2. Select a sequence and annotate it.
  3. Propagate the features and edit results.

Continue reading “Feature propagation in BankIt: easily annotate many sequences at once for GenBank submission”

GenBank submitters, is your genome assembly within the expected size range?

Validation issues can delay the processing of your submissions to GenBank. To avoid one type of delay, use the new “expected genome size” API to check the length of your genome assembly before submission.

The API compares the size of submitted genome assemblies to the expected genome size range for the species to identify outliers that can result from errors such as:

  • incorrect organism assignment
  • metagenome submitted as an organism genome
  • targeted sub-genome assembly not flagged as partial genome representation
  • gross contamination with other sequences

You can check in advance for these possible problems using the API. The API accepts the taxid for the species (taxid = Taxonomy ID – see our Taxonomy quick start guide on how to find the taxid for a given species) and the length of your assembly (excluding gaps and runs of Ns) as input and returns XML with the expected length, the acceptable range, and a status that tells you whether your assembly is too large, too small, or within the acceptable range. Look for <length_status>within_range</length_status> which confirms that your sequence passes the test!

Try the following examples:

https://api.ncbi.nlm.nih.gov/genome/v0/expected_genome_size?species_taxid=1773&length=4.41M
https://api.ncbi.nlm.nih.gov/genome/v0/expected_genome_size?species_taxid=562&length=7221235
https://api.ncbi.nlm.nih.gov/genome/v0/expected_genome_size?species_taxid=5476&length=5.72M

For more information, see the Genome Size Check documentation.

New release of the Prokaryotic Genome Annotation Pipeline now available

We have released a new version of the Prokaryotic Genome Annotation Pipeline (PGAP), available on GitHub. The new release includes the ability to ignore pre-annotation validation errors (–ignore-all-errors). This new feature allows you to produce a preliminary annotation for a draft version of the genome, even one that contains vector and adapter sequences or that is outside of the size range for the species. This draft annotation should be helpful with your ongoing work on the genome assembly. Please keep in mind that these pre-annotations and assemblies with contaminants or other errors are not suitable for submission to GenBank.

Another new feature allows you to provide the name of the consortium that generated the assembly and annotation so that this information appears in the final GenBank records. For more details, consult our guidelines on input files.

See our previous post and our documentation for details on how to obtain and run PGAP yourself.

Next on our to-do list is a module for calculating Average Nucleotide Identity (ANI) to confirm the assembly’s taxonomic assignment. Stay tuned!

Genome Workbench 3.0, now with support for preparing GenBank genome submissions

Genome Workbench version 3.0 (release notes) is now available. An important new feature is the submission preparation wizard that allows you to prepare prokaryotic and eukaryotic genome sequences for submission to GenBank. This wizard is the first step toward offering a better alternative to the Sequin submission tool.

You simply load your sequences into Genome Workbench and use the submission wizard to enter information about your submission through a set of dialog boxes and then save a submission-ready data file.  The package also includes tools for editing your sequences, annotation, and metadata.

See the tutorial video on our YouTube channel or the Genome Workbench documentation for more details on how to enable the wizard and prepare a submission.

Try our new SRA data management tools!

Have you ever needed to correct or improve SRA metadata after submitting, change the release date for your data or share your data with reviewers? Now you can perform these tasks yourself using the SRA data management features now LIVE in Submission Portal!

If you have an SRA submission and associated BioProject and BioSample, you can log into the Submission Portal, go to the Manage data tab, click into that BioProject and easily perform the following common tasks (Figure 1).

Continue reading “Try our new SRA data management tools!”

Prokaryotic Genome Annotation Pipeline (PGAP) now produces results suitable for submission to GenBank

We are happy to announce that you can now submit your genome sequences annotated by  your own local copy of the standalone Prokaryotic Genome Annotation Pipeline (PGAP) to GenBank.

How does it work? Download PGAP from GitHub, provide some basic information and the FASTA sequences for your genome sequence, and run the pipeline on your own machine, compute farm or the cloud. PGAP will produce annotation consistent with NCBI’s internal PGAP. Submit the resulting annotated genome to GenBank through the genome submission portal, and get an accession back.

As with any other submitted assembly, PGAP-annotated genomes will be screened for foreign contaminants and vector sequences at submission.  Any annotated assemblies that don’t pass may need to be modified. We are developing an automated process to handle these edits!

We are also working on other  improvements to stand-alone PGAP such as a module for calculating Average Nucleotide Identity (ANI) to confirm the assembly’s taxonomic assignment. Stay tuned for new developments!

 

Proposed changes to AGP files for genome assemblies

If you are a consumer or producer of AGP (A Golden Path) files for genome assemblies, please read on.  We’d like your feedback on the proposed changes described here.

As you know, AGP files are used to describe the structure of certain genome assemblies. The AGP file format has not kept up with changes in sequencing technology or International Sequence Database Collaboration (INSDC) feature usage. NCBI is therefore proposing to extend the current AGP v2.0 specification to add new linkage evidence types and a gap type of “contamination” as detailed below and described in the AGP v2.1 proposed specification.

Continue reading “Proposed changes to AGP files for genome assemblies”