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Table 1 Mean Index swapping rates by library prep method and machine type

From: Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Library type

Method description

Multiplex PCR prior to sequencing?

Mean library yield

Index swap rate (%)a

MiSeq

HiSeqX or 4000

NovaSeqb

PCR-free genomes

DNA shearing + adapter ligation

-

2.8 nM

0.13 ± 0.08

3.01 ± 0.91

4.85 ± 0.88

PCR-plus genomes

DNA shearing + adapter ligation

-

141.1 nM

0.03 ± 0.04

0.24 ± 0.06

no data

Somatic exome

DNA shearing + adapter ligation

+

354.2 nM

0.67 ± 0.08

0.83 ± 0.23

0.52%

Germline exome

Nextera transposase

+

286.2 nM

0.49 ± 0.12

0.68 ± 0.19

no data

Stranded mRNA

cDNA prep + adapter ligation

-

39.8 nM

0.01 ± 0.001

0.32 ± 0.02

no data

  1. aAll swap rate values for each library type are means of 8 different pool & flowcell observations
  2. bAs of submission, NovaSeq data had only been generated for PCR-free genomes and one flow cell of exomes