About the quality standard

As the European branch of the EBP project, ERGA is aligned with its genome assembly standards.

Briefly, the following metrics and criteria are to be considered in particular:

Contiguity

• Contig N50
• Scaffold N50

Correctness

• Quality Value (QV)

Completeness

• Single-copy genes presence (BUSCO)
• Kmer Completeness

Other criteria

• % Sequence assigned to candidate chromosomal sequences
• Gaps/Gbps
• Sex chromosome identification

Contiguity and Correctness metrics can be summarised with the EBP quality format: log10(Cont_N50).log10(Scaf_N50).Q(QV_value)

log10(10,000)=4, log10(100,000)=5, log10(1,000,000)=6, log10(10,000,000)=7 ...

If N50 is "chromosomal scale", then the log10 value is replaced by a C.

Standards for different scenarios

Minimum requirements are different depending on sample characteristics (sufficient tissue for DNA extraction) and genomic size (chromosomal N50 < 1 Mbp). Please have a look at the EBP Report on Assembly Standards for further details. The following table summarises the proposed metric values in each case:

Further notes

Sometimes, not all the metrics can be met (e.g., low BUSCO score due to a taxonomic group not being well represented).