Basis of differentiation | Long-read sequencing | Short-read sequencing |
Read length | Generates much longer DNA or RNA fragments, typically spanning a few thousand to several thousand base pairs | Generates relatively shorter DNA or RNA fragments, typically ranging from 50 to 300 base pairs in length |
Input DNA requirements | Medium to high | Low |
Throughput | Lower throughput capabilities due to longer run times and lower read output | Higher throughput capabilities due to shorter run times and higher read output |
Unique characteristic | Has the ability to analyze long stretches of DNA or RNA in a single read | Enables simultaneous sequencing of a large number of short fragments in a single run |
Genome assembly | Facilitates the assembly of complete genomes | Fragmented assemblies make it challenging to reconstruct entire genomes |
Detection of structural variations | Excels at detecting large structural variations | Limited ability to identify complex structural variations, especially large ones |
Ability to capture entire genomic regions | Is able to capture entire genomic regions | Has limited ability to capture complex genomic structures |
Base accuracy | Generally lower due to higher error rates inherent in long-read technologies | Generally higher due to shorter read lengths and more established error correction methods |
Cost-Effectiveness | Higher operating costs due to higher instrument and reagent costs as well as longer run times | More cost-effective due to lower cost per base and higher throughput, but can be expensive for large-scale projects |
Advantages |
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Ideal for | Investigation of complex genomic regions such as structural variants, repetitive regions, and large-scale genomic rearrangements | Targeting sequencing, transcriptomics, and variant detection |