INSDC standards for genome assembly submission

The original site; INSDC standards for genome assembly submission 2013.08.14 version

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.

Figure I. Three typical assembly processes

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.

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	One of, as appropriate, optional	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

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 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	One of, as appropriate, optional	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 annotation rules, including the requirement for presentation of the new/updated genome assembly in a peer reviewed publication prior to public release from INSDC.