The Long March: A Sample Preparation Technique that Enhances Contig Length and Coverage by High-Throughput Short-Read Sequencing
Author Information
Author(s): Katherine Sorber, Charles Chiu, Dale Webster, Michelle Dimon, J. Graham Ruby, Armin Hekele, Joseph L. DeRisi
Primary Institution: University of California San Francisco
Hypothesis
Can a new sample preparation method improve contig lengths and coverage in high-throughput short-read sequencing?
Conclusion
The long march technique significantly increases both contig lengths and target sequence coverage in high-throughput sequencing.
Supporting Evidence
- The long march increased the number of genomic bases covered by 39% in Plasmodium falciparum.
- The method also improved coverage of hepatitis B virus by 42%.
- Average contig size increased from 59 nt to 69 nt with the long march.
- The long march produced 17 contigs longer than 1000 nt, compared to 7 from the initial library.
Takeaway
The long march is a new way to prepare DNA samples that helps scientists read longer pieces of DNA and get more complete information from their tests.
Methodology
The long march method uses a Type IIS restriction enzyme to create nested sub-libraries from an initial amplicon library, enhancing sequencing results.
Potential Biases
Potential biases in sample preparation could affect the results.
Limitations
The long march protocol may not be optimized for all applications and relies on specific enzyme efficiencies.
Digital Object Identifier (DOI)
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