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Term: description of sequencing reads preprocessing (data_preproc_desc)

Description of preprocessing performed on the reads in the sequencing data file. Describe any in silico processing or modification of the sequencing reads away from the original state as received from the sequencer. This should include details such as adapter-, barcode-, and/or quality- trimming, or any filtering such as for read length or of off-target reads.

URI: MIXS:0001398

Applicable Checklists and Extensions

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

Name Description Checklist/Extension
Ancient A collection of terms appropriate when collecting samples and sequencing samp... Extension
MimsHostAssociatedAncient MIxS Data that comply with the Mims checklist, and HostAssociated and Ancient... -
MimsHumanAssociatedAncient MIxS Data that comply with the Mims checklist, and HumanAssociated and Ancien... -
MimsHumanOralAncient MIxS Data that comply with the Mims checklist, and HumanOral and Ancient exte... -
MimsHumanGutAncient MIxS Data that comply with the Mims checklist, and HumanGut and Ancient exten... -
MimsHumanSkinAncient MIxS Data that comply with the Mims checklist, and HumanSkin and Ancient exte... -
MimsSedimentAncient MIxS Data that comply with the Mims checklist, and Sediment and Ancient exten... -
MimsSoilAncient MIxS Data that comply with the Mims checklist, and Soil and Ancient extension... -
MimsPlantAssociatedAncient MIxS Data that comply with the Mims checklist, and PlantAssociated and Ancien... -

Properties

  • Range: String
  • Cardinality: 0..1 recommended

Examples

Value
Adapter trimmed, quality filtered, and host reads removed through mapping for ethical reasons.
Adapters removed by Trimmomatic (v0.39), and off-target reads removed after mapping to the HG19 Human reference with bwa aln (v0.7.19).
Demultiplexed with bcl2fastq, inline barcodes removed, and reads quality filtered with fastp (v1.0.0).

Annotations

  • Expected_value: description of any modifications to data away from original raw files

LinkML Source

name: data_preproc_desc
annotations:
  Expected_value:
    tag: Expected_value
    value: description of any modifications to data away from original raw files
description: Description of preprocessing performed on the reads in the sequencing
  data file. Describe any in silico processing or modification of the sequencing reads
  away from the original state as received from the sequencer. This should include
  details such as adapter-, barcode-, and/or quality- trimming, or any filtering such
  as for read length or of off-target reads.
title: description of sequencing reads preprocessing
examples:
- value: Adapter trimmed, quality filtered, and host reads removed through mapping
    for ethical reasons.
- value: Adapters removed by Trimmomatic (v0.39), and off-target reads removed after
    mapping to the HG19 Human reference with bwa aln (v0.7.19).
- value: Demultiplexed with bcl2fastq, inline barcodes removed, and reads quality
    filtered with fastp (v1.0.0).
in_subset:
- sequencing
from_schema: https://w3id.org/mixs
keywords:
- data analysis
- data
slot_uri: MIXS:0001398
domain_of:
- Ancient
- MimsHostAssociatedAncient
- MimsHumanAssociatedAncient
- MimsHumanOralAncient
- MimsHumanGutAncient
- MimsHumanSkinAncient
- MimsSedimentAncient
- MimsSoilAncient
- MimsPlantAssociatedAncient
range: string
required: false
recommended: true
multivalued: false