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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 large subunit (LSU) RNA, small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether it is a eukaryotic or prokaryotic genome, respectively. 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
MigsVi Minimal Information about a Genome Sequence: virus Checklist
MigsOrg Minimal Information about a Genome Sequence: organelle Checklist
Mimag Minimum Information About a Metagenome-Assembled Genome Checklist
Miuvig Minimum Information About an Uncultivated Virus Genome Checklist
MigsPl Minimal Information about a Genome Sequence: plasmid Checklist
Mims Metagenome or Environmental Checklist
Misag Minimum Information About a Single Amplified Genome Checklist
MigsEu Minimal Information about a Genome Sequence: eukaryote Checklist
MigsBa Minimal Information about a Genome Sequence: cultured bacteria/archaea Checklist
Agriculture A collection of terms appropriate when sequencing samples obtained in an agri... Extension

Properties

Examples

Value
High-quality draft genome

LinkML Source

name: assembly_qual
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 large subunit (LSU) RNA, small subunit
  (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether it is a eukaryotic
  or prokaryotic genome, respectively. 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
slot_uri: MIXS:0000056
alias: assembly_qual
domain_of:
- MigsBa
- MigsEu
- MigsOrg
- MigsPl
- MigsVi
- Mimag
- Mims
- Misag
- Miuvig
- Agriculture
range: AssemblyQualEnum