|Illumina DNA PCR-Free Prep||TruSeq DNA PCR-Free||TruSeq DNA Nano||Illumina DNA Prep|
|Assay Time||~1.5 hours||5 hours total assay time||~6 hours total assay time||~3-4 hours (from DNA extraction to normalized library)|
|Automation Capability||Liquid Handling Robots||Liquid Handling Robots||Liquid Handling Robots||Liquid Handling Robots|
|Input Quantity||25 ng to 300 ng||1 ug DNA||100 ng genomic DNA||Small genomes (e.g. microbial): 1-500 ng DNA. Large genomes (e.g. human): 100-500 ng DNA. (For blood and saliva, see the reference guide).|
|Mechanism of Action||Bead-linked transposome||Mechanical DNA fragmentation and adapter ligation. Workflow is PCR-free and gel-free.||Mechanical DNA fragmentation and adapter ligation. Workflow uses reduced-bias PCR and is gel-free.||Bead-linked transposome|
|Method||De Novo Sequencing , Whole-Genome Sequencing||Genotyping by Sequencing , Shotgun Sequencing , Whole-Genome Sequencing||Genotyping by Sequencing , Shotgun Sequencing , Whole-Genome Sequencing||Amplicon Sequencing , De Novo Sequencing , Shotgun Sequencing , Whole-Genome Sequencing|
|Multiplexing||Up to 384-plex||Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations (available soon)||Up to 24 single, 96 combinatorial (CD) dual, 24 unique dual and 96 unique dual (UD) combinations (available soon)||Up to 384 unique dual (UD) combinations and 96 combinatorial dual (CD) combinations|
|Nucleic Acid Type||DNA||DNA||DNA||DNA|
|Specialized Sample Types||Blood, Low-Input Samples, Not FFPE-Compatible, Saliva||Not FFPE-Compatible||Low-Input Samples, Not FFPE-Compatible||Blood, Not FFPE-Validated, Saliva|
The Illumina DNA PCR-Free Library Prep Kit provides superior read coverage across the GC-rich promoter region of the human RNPEPL1 gene, as compared to TruSeq DNA PCR-Free and TruSeq DNA Nano Library Prep Kits. Read maps were visualized with the Integrative Genomics Viewer (IGV) App, available in BaseSpace Sequence Hub.
Illumina DNA PCR-Free libraries prepared from a range of DNA inputs demonstrate (A) passing quality specifications for all DNA inputs and (B) equivalent callability performance. Q30 score = an inferred base call accuracy of 99.9%, autosome callability = the percentage of non-N reference positions in autosomal chromosomes with a passing genotype call, exon callability = the percentage of non-N reference positions in exons with a passing genotype call, SNPs = single nucleotide polymorphisms, indel = insertion-deletion mutation, precision (accuracy) = calculated as the ratio of [# of True Positive Calls/(# of True Positive Calls + # of False Positive Calls)], recall (sensitivity) = calculated as the ratio of [# of True Positive Calls/(# of True Positive Calls + # of False Negative Calls)]. Note: the lower limit sample input specifications for Illumina DNA PCR-Free have not been finalized.