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Table 3 Performance of different commercially available library preparation kits for 30X human genome builds

From: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

Parameter Library Preparation Kit
Nextera DNA Flex TruSeq Nano NEBNext Ultra Kapa HyperPlus Kapa HyperPrep TruSeq DNA PCR-free
No. samples 30 20 4 4 4 6
Includes PCR in protocol Yes Yes Yes Yes Yes No
Fragmentation method BLT Sonication Enzymatic Enzymatic Sonication Sonication
Input direct from blood and saliva Yes No No No No No
Incorporates normalization for inputs ≥100 ng Yes No No No No No
Total assay time, hours 3.5 11 6 6 6 10
Total PF PE reads 3.70E + 08 3.70E + 08 3.70E + 08 3.70E + 08 3.70E + 08 3.70E + 08
Diversity 3.1E + 09 2.0E + 09 1.3E + 09 2.8E + 09 4.6E + 09 1.9E + 09
Autosome coverage at 15X, % 97.9 98.0 97.8 96.1 91.3 98.1
Autosome callability, % 96.7 96.9 96.8 96.6 96.2 96.9
Autosome exon callability, % 98.7 98.4 98.8 98.7 98.5 99.0
SNV recall, % 98.7 98.7 98.8 98.5 97.8 98.8
SNV precision, % 99.8 99.7 99.7 99.1 94.4 99.9
Indel recall, % 94.2 92.9 94.5 93.1 91.0 95.9
Indel precision, % 97.2 94.9 97.7 97.6 96.1 98.3
  1. Libraries were prepared from 100 ng of human gDNA (NA12878) and sequenced on a HiSeqX with 6 samples per flow cell. Data presented is the average of the number of samples indicated for each kit. Data analysis was performed using the BaseSpace Sequence Hub Whole Genome Sequencing 6.0.0 and VCAT 3.0.0 Apps. Callability describes the percentage of base calls in the data set that pass the quality metrics required for making a genotype call; base quality, alignment quality, and minimum coverage levels are considered. Total assay time indicates the time from DNA extraction to library normalization and pooling, with workflow step times determined using specific methods: DNA extraction (QIAamp DNA Mini Kit or Flex Lysis Kit), DNA quantitation (Qubit), DNA fragmentation (Covaris), and manual library normalization and pooling (Bioanalyzer). Calculations assumed that 16 samples were processed at a time with a multichannel pipette. BLT Bead-linked transposome, PE Paired-end, PF Pass filter, SNV Single-nucleotide variant, Indel Insertion/deletion