QC Checks and Metrics for Illumina Next Generation Sequencing Data

Listing of Directories

lib

• npg_qc::Schema namespace - DBIx ORM
• npg_qc::illumina namespace - db loaders for Illumina QC metrics
• npg_qc::autoqc namespace - WSI core sequencing pipeline in-house QC checks and storage of QC metrics
• npg_qc::mqc - evaluation and reporting of QC metrics

bin

Perl scripts which are deployed to the production environment

scripts

Supplementary scripts, not deployed

t

Tests, test data, supplementary scripts and modules for testing

npg_qc_viewer

Source code for the web server that displays the QC metrics

docs

Documentation, useful code snippets

NPG QC database

Legacy Data

QC metrics and evaluation outcomes for all production Illumina sequencing runs are stored in a relational database. This database has four legacy tables, recipe_file, run_and_pair, run_info, run_recipe, for which we do not generate ORM classes. No code is using these tables. The data is kept for auditing perposes. The size of these tables is small in comparison with the size of the rest of the tables. The overhead of moving these old tables to a different storage is not justified.