Enum: SequencingApplication

Primary applications or assays using DNA/RNA sequencing

Permissible Values

Value	Meaning	Description
WHOLE_GENOME_SEQUENCING	EDAM:topic_3673	Whole genome sequencing (WGS)
WHOLE_EXOME_SEQUENCING	EDAM:topic_3676	Whole exome sequencing (WES)
TRANSCRIPTOME_SEQUENCING	EDAM:topic_3170	RNA sequencing (RNA-seq)
TARGETED_SEQUENCING	None	Targeted gene panel sequencing
EPIGENOMICS	None	Epigenomic profiling
METAGENOMICS	EDAM:topic_3837	Metagenomic sequencing
SINGLE_CELL_GENOMICS	None	Single-cell genomics
SINGLE_CELL_TRANSCRIPTOMICS	EDAM:topic_4028	Single-cell transcriptomics
CHROMATIN_IMMUNOPRECIPITATION	EDAM:topic_3656	ChIP-seq
CHROMATIN_ACCESSIBILITY	None	ATAC-seq/FAIRE-seq
DNA_METHYLATION	None	Bisulfite/methylation sequencing
CHROMOSOME_CONFORMATION	None	Hi-C/3C-seq
VARIANT_CALLING	None	Genetic variant discovery
PHARMACOGENOMICS	None	Pharmacogenomic sequencing
CLINICAL_DIAGNOSTICS	None	Clinical diagnostic sequencing
POPULATION_GENOMICS	None	Population-scale genomics

Slots

Name	Description
sequencing_application	Primary applications or assays using DNA/RNA sequencing

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: SequencingApplication
description: Primary applications or assays using DNA/RNA sequencing
title: Sequencing Applications
from_schema: https://w3id.org/linkml/valuesets
rank: 1000
permissible_values:
  WHOLE_GENOME_SEQUENCING:
    text: WHOLE_GENOME_SEQUENCING
    description: Whole genome sequencing (WGS)
    meaning: EDAM:topic_3673
    title: WHOLE_GENOME_SEQUENCING
  WHOLE_EXOME_SEQUENCING:
    text: WHOLE_EXOME_SEQUENCING
    description: Whole exome sequencing (WES)
    meaning: EDAM:topic_3676
    title: WHOLE_EXOME_SEQUENCING
    aliases:
    - Exome sequencing
  TRANSCRIPTOME_SEQUENCING:
    text: TRANSCRIPTOME_SEQUENCING
    description: RNA sequencing (RNA-seq)
    meaning: EDAM:topic_3170
    title: TRANSCRIPTOME_SEQUENCING
    aliases:
    - RNA-Seq
  TARGETED_SEQUENCING:
    text: TARGETED_SEQUENCING
    description: Targeted gene panel sequencing
  EPIGENOMICS:
    text: EPIGENOMICS
    description: Epigenomic profiling
  METAGENOMICS:
    text: METAGENOMICS
    description: Metagenomic sequencing
    meaning: EDAM:topic_3837
    title: METAGENOMICS
    aliases:
    - Metagenomic sequencing
  SINGLE_CELL_GENOMICS:
    text: SINGLE_CELL_GENOMICS
    description: Single-cell genomics
  SINGLE_CELL_TRANSCRIPTOMICS:
    text: SINGLE_CELL_TRANSCRIPTOMICS
    description: Single-cell transcriptomics
    meaning: EDAM:topic_4028
    title: SINGLE_CELL_TRANSCRIPTOMICS
    aliases:
    - Single-cell sequencing
  CHROMATIN_IMMUNOPRECIPITATION:
    text: CHROMATIN_IMMUNOPRECIPITATION
    description: ChIP-seq
    meaning: EDAM:topic_3656
    title: CHROMATIN_IMMUNOPRECIPITATION
    aliases:
    - Immunoprecipitation experiment
  CHROMATIN_ACCESSIBILITY:
    text: CHROMATIN_ACCESSIBILITY
    description: ATAC-seq/FAIRE-seq
  DNA_METHYLATION:
    text: DNA_METHYLATION
    description: Bisulfite/methylation sequencing
  CHROMOSOME_CONFORMATION:
    text: CHROMOSOME_CONFORMATION
    description: Hi-C/3C-seq
  VARIANT_CALLING:
    text: VARIANT_CALLING
    description: Genetic variant discovery
  PHARMACOGENOMICS:
    text: PHARMACOGENOMICS
    description: Pharmacogenomic sequencing
  CLINICAL_DIAGNOSTICS:
    text: CLINICAL_DIAGNOSTICS
    description: Clinical diagnostic sequencing
  POPULATION_GENOMICS:
    text: POPULATION_GENOMICS
    description: Population-scale genomics