Once samples pass initial sequencing quality metrics generated by the sequencers, they are assessed by FASTQC that checks for per-base sequence quality, GC content, and N content, among others. If the data indeed looks sub-par, they will be immediately reprepped and resequenced. Data contamination is checked using FastQ Screen.
Data trimming is done if needed using any one of:
Our quality control process also included assessing per base coverage, mean coverage, and on target percentages, among others. These will be discussed in the Useful Metrics section.