Term: assembly quality (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

URI: MIXS:0000056

Applicable Checklists and Extensions

NOTE: does not include Combinations (of checklists and extensions) that use assembly_qual.

Name	Description	Checklist/Extension
Agriculture	A collection of terms appropriate when sequencing samples obtained in an agri...	Extension
MigsEu	Minimal Information about a Genome Sequence: eukaryote	Checklist
Misag	Minimum Information About a Single Amplified Genome	Checklist
MigsBa	Minimal Information about a Genome Sequence: cultured bacteria/archaea	Checklist
MigsVi	Minimal Information about a Genome Sequence: virus	Checklist
Mimag	Minimum Information About a Metagenome-Assembled Genome	Checklist
MigsOrg	Minimal Information about a Genome Sequence: organelle	Checklist
MigsPl	Minimal Information about a Genome Sequence: plasmid	Checklist
Miuvig	Minimum Information About an Uncultivated Virus Genome	Checklist
Mims	Metagenome or Environmental	Checklist

Properties

• Range: String
• Cardinality: 0..1

Examples

Value
High-quality draft genome

Annotations

• Expected_value: enumeration

LinkML Source

name: assembly_qual
annotations:
  Expected_value:
    tag: Expected_value
    value: enumeration
description: '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'
title: assembly quality
examples:
- value: High-quality draft genome
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- quality
string_serialization: '[Finished genome|High-quality draft genome|Medium-quality draft
  genome|Low-quality draft genome|Genome fragment(s)]'
slot_uri: MIXS:0000056
alias: assembly_qual
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: string