| Technology | Illumina (50-300 bp) | PacBio, Oxford Nanopore (several kb to Mb) |
| Accuracy | High accuracy, low error rate | Higher error rate (but improving) |
| Throughput | High throughput, large data volume | Lower throughput |
| Cost | Lower cost per base | Higher cost per base |
| Assembly | Difficult to assemble repetitive or complex regions | Better assembly, resolves complex regions |
| Structural Variants | Limited detection of large variants | Superior for detecting large structural variants |
| Phasing | Limited contiguity, harder to phase alleles | Easier to phase alleles due to longer read length |
| Variant Calling | Excellent for small variants (SNPs, small indels) but struggles with larger structural variants and complex regions. Bias: Prone to GC bias and difficulties in highly repetitive regions. | Good for detecting large structural variants and complex variants, but higher error rates affect base-level accuracy. Bias: More random errors, but less GC bias. |
| Best Use Cases | Resequencing, transcriptomics, population studies | De novo assembly, structural variation, complex genomes |