Instructions

The InsertSize is considered for PairedEnd-Mode:

  • effectiveReadLength = ReadLength - R1_R2_Overlap

Number of reads for is calculation is reduced by:

  • Unassigned Reads due to unmatched barcodes (default: 3%)
  • Unspecific Reads (don’t map in the target region, default OnTargetRate: 80%, set it to 100% for WholeGenome-Sequencing)

Target Sizes of different Whole Exome Kits

KitName Size in Mb
Agilent SureSelect V5 50
Agilent SureSelect V5 + UTR 75
Agilent SureSelect V6 60
Agilent SureSelect V6 + Cosmiq 66
Agilent SureSelect V6 + UTR 91

Reads per Lane on different Illumina Instruments

InstrumentType/Mode Reads in M
MiSeq, normal FlowCell v3 20
MiSeq, Micro FlowCell v3 4
MiSeq, Nano FlowCell v3 1
NextSeq500_MidOutput 150
NextSeq500_HighOutput 400
NextSeq2000 P1 100
NextSeq2000 P2 400
NextSeq2000 P3 1200
NovaSeq_SP 650
NovaSeq_S1 1300
NovaSeq_S2 3300
NovaSeq_S4 8000
TODO
  • include Mapping Rate