Sequencing

Summary of SMaHT Portal object type Sequencing . Types referencing this type are: AlignedReads, File, FileSet, HistologyImage, OutputFile, ReferenceFile, SubmittedFile, SupplementaryFile, UnalignedReads, VariantCalls. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.


Description: Sequencing items contain information on the sequencing of libraries.

Tip

See actual Sequencing data here

Required Properties

Property Type Description
read_type string See below for more details.
sequencer Sequencer
string 		See below for more details.
submission_centers SubmissionCenter
array of string 		See below for more details.
See values here
submitted_id string See below for more details.
target_read_length integer See below for more details.

Identifying Properties

Property Type Description
accession string See below for more details.
submitted_id string See below for more details.
uuid string See below for more details.

Reference Properties

Property Type Description
consortia Consortium
array of string 		See below for more details.
See values here
preparation_kits PreparationKit
array of string 		See below for more details.
protocols Protocol
array of string 		See below for more details.
sequencer Sequencer
string 		See below for more details.
submission_centers SubmissionCenter
array of string 		See below for more details.
See values here

Properties

Property Type Description
accession string A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.]
alternate_accessions array of string
• restricted
 Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.]
consortia Consortium
• array of string
• unique
 Consortia associated with this item.
See values here
display_title string
• calculated
 -
flow_cell string Flow cell used for sequencing.
movie_length integer
• min value: 0
 Length of movie used in sequencing (hours).
on_target_rate number
• min value: 0
 An expected ratio, the number of reads with enrichment signals for the targeted element versus the overall reads sequenced. Relevant for target capture sequencing.
preparation_kits PreparationKit
• array of string
• unique
 Links to sequencing preparation kits.
protocols Protocol
• array of string
• min items: 1
• unique
• restricted
 Protocols providing experimental details.
read_type
 • Not Applicable
 • Paired-end
 • Single-end 		enum of string Type of reads obtained from sequencing.
sequencer Sequencer
• string
 Instrument used for sequencing.
status
 • deleted
 • draft
 • in review ← default
 • obsolete
 • public
 • released
 • restricted 		enum of string
• default: in review
 -
submission_centers SubmissionCenter
• array of string
• unique
 Submission Centers that created this item.
See values here
submitted_id string Unique identifier for the item assigned by the submitter.
Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_SEQUENCING_[A-Z0-9-_.]{4,}$
tags array of string
• min string length: 1
• max string length: 50
• unique
• restricted
 Key words that can tag an item - useful for filtering.
Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$
target_coverage number
• min value: 0
 Expected coverage for the sequencing. For Duplex sequencing, this applies to the target duplex coverage for sequencing.
target_monomer_length integer
• min value: 0
 Target monomer length for Kinnex/MAS-Seq (bp).
target_read_count integer
• min value: 0
 Expected read count for the sequencing, in read pairs if paired-end.
target_read_length integer
• min value: 0
 Expected read length for the sequencing (bp).
uuid string Unique ID by which this object is identified.