Sequencing protocol

Local machine namesequencing_protocol.local_machine_name (string) Local name for the particular machine used for sequencing. For example "Machine1" or "HSMA-20".

Paired endRequiredsequencing_protocol.paired_end (boolean) Whether the sequenced molecule was sequenced from both ends. For example "Should be one of: yes, or no.".

Sequencing protocol>10x-specific (10x object) Fields specific for 10x experiments.

Drop uniformitysequencing_protocol.10x.drop_uniformity (boolean from 10x) Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run. For example "Should be one of: yes, or no.".

Fastq creation methodsequencing_protocol.10x.fastq_method (string from 10x) Method used for the generation of fastq files from bcl files. For example "Cellranger mkfastq" or "bcl2fastq2".

Fastq creation method versionsequencing_protocol.10x.fastq_method_version (string from 10x) Version of the program used for fastq generation. For example "Cellranger 2.1.1" or "v2.20".

Pooled channelssequencing_protocol.10x.pooled_channels (number from 10x) The number of channels pooled within a sequencing lane. For example "4".

Sequencing protocol>Instrument manufacturer and modelRequired (instrument_ontology object) The manufacturer and model of the sequencer.

Instrument ontology IDsequencing_protocol.instrument_manufacturer_model.ontology (string from instrument_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0008565" or "EFO:0008632".Graph restriction: Subclasses of EFO:0000548 from obo:efo.

Instrument ontology labelsequencing_protocol.instrument_manufacturer_model.ontology_label (string from instrument_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "Illumina HiSeq 2500" or "ONT MinION".

InstrumentRequiredsequencing_protocol.instrument_manufacturer_model.text (string from instrument_ontology) The full name of the instrument used. For example "Illumina HiSeq 2500" or "ONT MinION".

Sequencing protocol>Sequencing methodRequired (sequencing_ontology object) The general method for sequencing.

Sequencing approach ontology IDsequencing_protocol.method.ontology (string from sequencing_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0008440" or "EFO:0008441".Graph restriction: Subclasses of OBI:0000070 from obo:efo.

Sequencing approach ontology labelsequencing_protocol.method.ontology_label (string from sequencing_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "tag based single cell RNA sequencing" or "full length single cell RNA sequencing".

Sequencing approachRequiredsequencing_protocol.method.text (string from sequencing_ontology) The name of a sequencing approach being used. For example "tag based single cell RNA sequencing" or "full length single cell RNA sequencing".

Sequencing protocol>Protocol coreRequired (protocol_core object) Core protocol-level information.

Document filenamesequencing_protocol.protocol_core.document (string from protocol_core) A filename of a PDF document containing the details of the protocol. For example "my_cool_protocol.pdf".

Protocol descriptionsequencing_protocol.protocol_core.protocol_description (string from protocol_core) A general description of the protocol.

Protocol IDRequiredsequencing_protocol.protocol_core.protocol_id (string from protocol_core) A unique ID for the protocol.

Protocol namesequencing_protocol.protocol_core.protocol_name (string from protocol_core) A short name for the protocol.

protocols.io DOIsequencing_protocol.protocol_core.protocols_io_doi (string from protocol_core) The protocols.io digital object identifier (doi) for the protocol. For example "10.17504/protocols.io.mgjc3un".

Publication DOIsequencing_protocol.protocol_core.publication_doi (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".

Sequencing protocol>provenance (provenance object) Provenance information provided by the system.

Accessionsequencing_protocol.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredsequencing_protocol.provenance.document_id (string from provenance) Identifier for document.

Schema major versionsequencing_protocol.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versionsequencing_protocol.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredsequencing_protocol.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDsequencing_protocol.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update datesequencing_protocol.provenance.update_date (string from provenance) When project was last updated.

Updater IDsequencing_protocol.provenance.updater_id (string from provenance) ID of individual who last updated project.