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Updated: Jul 14, 2026
10:34
Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
Whole-genome sequencing and assembly with high-throughput, short-read technologies
Andreas Sundquist1, Mostafa Ronaghi, Haixu Tang
1Department of Computer Science, Stanford University, Stanford, California, United States of America. asundqui@cs.stanford.edu
Plos One
|May 31, 2007
Summary
We developed a novel Short Read Assembly Protocol (SHRAP) for de novo sequencing of large genomes using short-read technologies. This method enables accurate genome assembly and paves the way for inexpensive mammalian genome sequencing.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Short-read sequencing technologies offer reduced costs but face limitations for de novo eukaryotic genome assembly.
- Standard shotgun sequencing protocols are insufficient for assembling complex genomes with short reads.
Purpose of the Study:
- To present the Short Read Assembly Protocol (SHRAP), a new sequencing protocol and assembly methodology for high-throughput short-read technologies.
- To enable cost-effective de novo sequencing of mammalian genomes.
Main Methods:
- A variation on hierarchical sequencing involving random clone library selection and high clone/low read coverage sampling.
- A three-stage assembly process: local assemblies, clone-sized assemblies, and chromosome-sized assemblies.
- Clone ordering to localize assembly problems and enable parallelization.
Main Results:
- Successfully assembled simulated reads from D. melanogaster and human chromosomes with large contiguous sequences and low misassembly rates.
- Developed an accurate clone-ordering method for D. melanogaster and the human genome.
- Demonstrated the feasibility of assembling short, unpaired reads from repetitive genomes.
Conclusions:
- SHRAP overcomes limitations of short-read technologies for de novo genome sequencing.
- The methodology facilitates inexpensive de novo sequencing of mammalian genomes.
- High-throughput short-read technologies combined with SHRAP will make large-scale genome sequencing more accessible.
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