Illimuna Sequencing Data QC at WSI
Most of data produced by Illumina sequencers go though manual assessment, which takes place after the run data went through the analysis pipeline, which is run by the Institute's core bioinformatics team, and before the data are deposited in the institute's archive. Metrics that are necessary for QC assessment are produced during the analysis.
The manual QC assessment is peformed by a special team within Sequencing Operations. Success of the sequencing process and quality of individual or pooled libraries is assesed separately. The criteria applied during the assessment do not necessary reflect all complexity of research projects and end-user requirements. After the data are archived, end users often perform their own assessment and are able to save its outcome in the database that supports the QC process. The outcome of these assessments is exported to the Institute's warehouse database as 1 for a pass and 0 for a fail.
iseq_run_lane_metrics qc_seq iseq_product_metrics qc_seq iseq_product_metrics qc_lib iseq_product_metrics qc_user iseq_product_metrics qc
qc_seq - assessment of sequencing process and pool deplexing level, granularity level - lane of a flowcell, performed by the manual QC team qc_lib - assessment of library quality, granularity - individual product (lane, plex or a merged product), performed by the manual QC team qc_user - assessment of product usability for a particular research project, performed either manually by the end user representative or automatically using criteria agreed with the project owners qc - an overall value for a product; a fail if any of the above qc outcomes are a fail, a pass if qc_user outcome is a pass or, when the qc user outcome is not defined, when both qc_lib and qc_seq are a pass, undefined if both qc_user and qc_lib are undefined and qc_seq is a pass
Other relevant code repositories: https://github.com/wtsi-npg/ml_warehouse, https://github.com/wtsi-npg/npg_ml_warehouse