INSDC standards for genome assembly submission

This page represents a brief document describing at a high level INSDC requirements for assembly submission. Differences in submission requirements at lower levels are possible between INSDC databases (DDBJ, NCBI and ENA) and we recommend submitters refer to the corresponding websites of the submitting databases for more detailed instructions.

Genome assemblies comprise a number of possible layers of information, including reads, contigs, scaffolds and chromosomes (see figure I). This document lays out the requirements for submission of genome assembly information into INSDC databases.

assembly_layers

Figure I. The figure shows three typical assembly processes and the layers of information that they yield. A) Clone-based assembly with scaffolding and finishing steps. B) Shotgun assembly direct to chromosomes. C) Partial assembly to contigs only.

 

Consistent with the variety of assembly processes, submitters to INSDC approach with data for the layers in different combinations of layers. Tables I and II shows requirements for new genome assembly submissions and updates to existing assembly submissions.

 

Table I. New genome assembly submissions

Component

Level

Comment

Reads

Recommended

Complete read and quality data

Read to contig mapping

One of, as appropriate, optional

e.g. BAM alignment of reads to contigs

Read to chromosome mapping

e.g. BAM alignment of reads to new chromosome

Contigs

At least one layer mandatory

 

Scaffolds

Chromosomes

Scaffold to chromosome  mapping

Mandatory if both layers are present

e.g. AGP file

Contig to scaffold mapping

Mandatory if both layers are present

e.g. AGP file

Assembly description

Mandatory

Brief information relating to assembly and future plans

Functional annotation

Optional

 

 

Table II. Update to existing genome assembly

Component

Level

Comment

Reads

Recommended

Complete read and quality data

Read to contig mapping

One of, as appropriate, optional

e.g. BAM alignment of reads to contigs

Read to chromosome mapping

e.g. BAM alignment of reads to new chromosome

Contigs

At least one layer mandatory, with highest layer no lower than for   existing assembly

 

Scaffolds

Chromosomes

Scaffold to chromosome mapping

Mandatory if both layers are present

e.g. AGP file

Contig to scaffold mapping

Mandatory if both layers are present

e.g. AGP file

Assembly description

Mandatory

Brief information relating to assembly and future plans

Regenerated (or lifted-over) functional annotation

Recommended

If associated with existing assembly

Coding annotation mappings between old and new assemblies

Recommended where functional annotation is provided for the updated   assembly

Typically through INSDC protein ID mappings

Third party genome assembly submissions and updates, in which the submitting group does not hold complete ownership of data, are subject to existing third party data rules, including the requirement for presentation of the new/updated genome assembly in a peer reviewed publication prior to public release from ENA.