Parallel short sequence assembly of transcriptomes
2009
Parallel Method for Transcriptome Assembly
Sample size: 925000000
publication
Evidence: high
Author Information
Author(s): Jackson Benjamin G, Schnable Patrick S, Aluru Srinivas
Primary Institution: Iowa State University
Hypothesis
Can a parallel method effectively assemble transcriptomes from large short sequence data sets?
Conclusion
The method successfully assembled 925 million sequences from 40 billion nucleotides in a few minutes using a 1024 processor Blue Gene/L.
Supporting Evidence
- The method can scale to large problem sizes.
- It processes high coverage data sets quickly.
- Validation was performed by aligning assembled contigs back to the reference genome.
Takeaway
This study shows a new way to quickly piece together DNA sequences from lots of tiny bits, helping scientists understand genes better.
Methodology
The method constructs a distributed bidirected graph to capture overlap information and uses parallel computing to manage complexity.
Limitations
The method may require integration of clone pairs for better genome assembly.
Digital Object Identifier (DOI)
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