Whole Genome Shotgun Sequence Submissions

DDBJ/EMBL/GenBank accepts contigs from ongoing Whole Genome Shotgun (WGS) sequencing projects. These records can contain annotations, and an entire project is updated as sequencing progresses.

See the list of WGS projects.

Table of Contents

• Introduction
• What To Do
• WGS Project
• How to Create a WGS Submission
• AGP Files to Build Scaffolds and/or Chromosomes
• Updating a WGS Project

Introduction

Each WGS project is assigned a stable 4-letter WGS project_ID, which does not change as the project is updated. In addition to the WGS project_ID, the contig identifiers have a version number corresponding to a particular project update. Finally, each individual contig within the assembly is assigned a unique accession number prefixed by the WGS project_ID and version number. For instance, if a project's assigned accession number is XXXX00000000, then that project's first assembly version would be XXXX01000000, and the first contig of that version would be XXXX01000001. (The last six digits of this ID identify each individual contig).

The nucleotide data from most WGS projects go into the BLAST wgs database, whereas proteins go into the BLAST nr database. Nucleotides from environmental projects are present in either the BLAST env_nt or wgs database, depending upon whether that sequence has been identified as a particular organism, or if the organism is not yet known. Similarly, the proteins from those projects are in the env_nr or nr BLAST database.

See the Metagenome Submission Guide for information about how to submit the various elements of a metagenome project.

What To Do

Examples (annotated records are shown as GenBank(Full) view in Entrez):

Annotated Contigs	Annotated Scaffolds	No Annotation
WGS contig with annotation	WGS contig without annotation	WGS contig without annotation
Chromosome CON with annotation	Chromosome CON with annotation	Chromosome CON without annotation
Scaffold CON with annotation	Scaffold CON with annotation	Scaffold CON without annotation

How to Create a WGS Submission

File Format

A sample definition line is
>SeqID [organism=Mus musculus] [strain=BALB/c] [tech=wgs] [chromosome=2]

Annotation can be included by creating a 5-column table in a .tbl file for each .fsa file. Go to the appropriate page for information about the format of the table and the desired annotation for eukaryotic or bacterial genomes. Three required fields are

• locus_tag for genes
• The locus_tag is the systematic name of the gene and is used for tracking individual genes. It therefore must be unique across all the genes in a project. If a gene's biological name is known, then it is included as the gene qualifier in the table.


• protein_id for proteins
• The protein_id is the SeqID of the protein (analogous to the nucleotide SeqID) and is used to track the protein. All of the SeqIDs, both nucleotide and protein, must be unique within a project. For WGS projects you can use type general protein_id's (format: gnl|dbname|SeqID) or local protein_id's (format: lcl|SeqID). Note that during our processing both forms of protein_id's are converted to type general id's in the format gnl|WGS:XXXX|SeqID, where XXXX is the project_ID.


• product for proteins
• The product is free text, chosen by the submitter. Protein names should be concise names, not descriptions or phrases. BLAST similarity results can be included as a note, or can be modified to be used as the product name. For example, if BLAST results indicate that the translation is similar to XYZ protein, then the product name could be "XYZ-like protein". If the protein is predicted and the product name is not known, use "hypothetical protein" as the product name.

Note that the nucleotide SeqID appears in the DEFINITION line in the flatfile view of the record. Although the protein SeqIDs are not displayed in the final flatfile view, they are present in the ASN.1.

See example *.fsa and *.tbl files for various situations, such as partial CDS or features on the minus strand.

Use tbl2asn to include the Phrap/Consed quality scores of a sequence. The scores must be in files named *.qvl that are in the same directory and have the same nucleotide SeqIDs as the corresponding *.fsa files.

Template File

If there is a published reference, it can be sent separately with the submission, to be added to the records by GenBank staff during WGS processing.

tbl2asn does not include a release date in the output file, so include that information in your email message to us when you submit.

Using tbl2asn

To create WGS submissions from multiple .fsa files, run tbl2asn with the command:

tbl2asn -t template.sbt -p path_to_files -v

Note that you must also specify the path as part of the template file's name if the template file is in a different directory than where you are running tbl2asn.

In a directory specified by '-p', the program looks for pairs of .fsa and .tbl files with the same file name prefix, for example file.fsa and file.tbl, and it builds ASN.1 records for these pairs. The ASN.1 record will be called file.sqn. The results of the validation (-v; error checking) will be called file.val. Most validation errors must be fixed before the .sqn files can be submitted to GenBank; however, taxonomy-related errors and "No publications anywhere" errors can generally be ignored.

If you wish to have GenBank flatfiles generated also, use the -b argument when you run tbl2asn, and a .gbf file will be generated for each .fsa file in the directory.

If you want to create a submission from only one particular .fsa file that is in a directory that contains multiple .fsa files, use the -i argument to indicate which file is to be read.

Go to the tbl2asn page for more detailed information about tbl2asn, its command line arguments, and file formats.

Multiple Sequences in a Single .fsa File

You can put multiple FASTA sequences (usually less than 10,000 sequences) into a single .fsa file if you wish to have fewer files. The corresponding .tbl file must have the annotation information for all of the sequences in the .fsa file. Run tbl2asn with the -s argument so that each definition line is recognized as the beginning of a new sequence. A single .sqn file will then be generated for the multiple sequences of each .fsa file.

See example .fsa and .tbl files.

AGP Files to Build Scaffolds and/or Chromosomes

If there is assembly information, of how the contigs are assembled into scaffolds (supercontigs) or chromosomes, then submit an AGP file with that information. AGP files provide the ordering and orientation information to construct supercontigs or scaffolds from contigs, or to construct chromosomes from supercontigs and/or contigs. More information about genome assemblies is here. See this page for the AGP format.

Some specific requests are: