|Instrument||Recommended Number of Samples||Read Length|
|NextSeq 550 System||Samples per run: high output: 8 samples per run (based on >95% covered at 30×)||2 x 151 bp|
|AmpliSeq for Illumina Exome Panel||TruSeq DNA Exome||Nextera DNA Exome||Illumina DNA Prep with Enrichment|
|Assay Time||< 7.5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)||2.5 days||< 2.5 days||~6.5 hours|
|Content Specifications||> 97% of CCDS||Captures coding exons. Covers 45 Mb of exonic content (≥98% of RefSeq, CCDS, and Ensembl coding content).||Captures coding exons. Covers 45 Mb of exonic content (≥98% of RefSeq, CCDS, and Ensembl coding content).||Exome: 45 Mb exonic content (≥98% of RefSeq, CCDS, and Ensembl coding content).
Custom: 0.5 - 15 Mb genomic content of interest.
Fixed panels: Content varies by panel.
|Description||Enables researchers to prepare 8 exome libraries in <7.5 hours with <1.5 hours hands-on time.||A cost-effective exome research workflow focused on ≥98% of RefSeq, CCDS, and Ensembl coding content.||A cost-effective exome research workflow focused on ≥98% of RefSeq, CCDS, and Ensembl coding content.||A fast, flexible research solution that enables whole-exome, custom, and fixed panel targeted sequencing.|
|Hands-On Time||< 1.5 hours||6 hours||3 hours||~2 hours|
|Input Quantity||50 ng minimum||100 ng genomic DNA||50 ng genomic DNA||10-1000 ng high-quality genomic DNA or 50-1000 ng FFPE DNA. (For blood and saliva, see the reference guide).|
|Mechanism of Action||Multiplex PCR||Mechanical fragmentation (Covaris) and exome enrichment with biotinylated capture probes||Transposase-based fragmentation and exome enrichment with biotinylated capture probes||Bead-bound transposomes and hybrid-capture chemistry|
|Method||Amplicon Sequencing , Exome Sequencing||Exome Sequencing||Exome Sequencing||Custom Sequencing, Exome Sequencing , Target Enrichment , Target Enrichment, Targeted DNA Sequencing|
|Multiplexing||96 dual index combinations||Up to 12-plex enrichment||Up to 12-plex enrichment||Up to 384 available unique dual indexes. Pre-enrichment pooling of up to 12-plex is tested.|
|On-Target Reads||>80%||>80%||>75%||≥85% (for exome panel)*|
|Specialized Sample Types||Not FFPE-Compatible||FFPE Tissue||Low-Input Samples, Not FFPE-Compatible||Blood, FFPE Tissue, Saliva|
|Species Category||Human||Human||Human||Human, Other|
|Uniformity||>90% (% coverage at 20x for 4 Gb)||>85% (% coverage at 20x for 4 Gb)||>75% (% coverage at 20x for 4 Gb)||≥90% (% coverage at 20x for 4 Gb; for exome panel)|