Skim Sequencing for Assessing Library Quality
Before committing to a large expensive sequencing run, some may prefer to get a preview of the quality of the results by sequencing at low depth. Several output metrics from the BD Rhapsody™ Sequence Analysis Pipeline can be evaluated while performing skim sequencing to assess library and sequencing run quality. Output metrics are stable at low sequencing depth (〜2 million sequencing reads or higher).
Metrics that are often stable with skim sequencing
Sequence Quality
- Pct_Read_Pair_Overlap
- Pct_Reads_Too_Short
- Pct_Reads_Low_Base_Quality
- Pct_Reads_High_SNF
- Pct_Reads_Filtered_Out
Library Quality
- Pct_Q30_Bases_in_Filtered_R2
- Pct_CellLabel_UMI
- Pct_CellLabel_UMI_Aligned_Uniquely
Cells
- Putative_Cell_Count
- Pct_Reads_from_Putative_Cells