Slot: assembly_qual
The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated
Domain and Range
None → 0..1 assembly_qual_enum
Parents
- is_a: sequencing field
Children
- ME➞assembly_qual
- MIGS bacteria➞assembly_qual
- MIGS eukaryote➞assembly_qual
- MIGS org➞assembly_qual
- MIGS plant➞assembly_qual
- MIGS virus➞assembly_qual
- MIMAG➞assembly_qual
- MISAG➞assembly_qual
- MIUVIG➞assembly_qual
Used by
Other properties
| Aliases: | assembly quality | |
| Mappings: | MIXS:0000056 | |
| Comments: | Expected value: enumeration | |
| Position: 54.0 | ||
| Examples: | Example(value='High-quality draft genome', description=None) | |
| See also: | https://github.com/GenomicsStandardsConsortium/mixs/issues/147 | |
| Exact Mappings: | MIGS: |