Minimus: a fast, lightweight genome assembler
Minimus: a fast, lightweight genome assembler
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Publication or External Link
Date
2007-02-26
Authors
Sommer, Daniel D.
Delcher, Arthur L.
Salzberg, Steven L.
Pop, Mihai
Advisor
Citation
Sommer, D.D., Delcher, A.L., Salzberg, S.L. et al. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 8, 64 (2007).
DRUM DOI
Abstract
Background: Genome assemblers have grown very large and complex in response to the need
for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the
most common uses of assemblers, however, are best served by a simpler type of assembler that
requires fewer software components, uses less memory, and is far easier to install and run.
Results: We have developed the Minimus assembler to address these issues, and tested it on a
range of assembly problems. We show that Minimus performs well on several small assembly tasks,
including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate
Minimus' performance in assembling bacterial genomes in order to assess its suitability as a
component of a larger assembly pipeline. We show that, unlike other software currently used for
these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more
fragmented assembly.
Conclusion: We find that for small genomes and other small assembly tasks, Minimus is faster and
far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly
suited to be a component of complex assembly pipelines. Minimus is released as an open-source
software project and the code is available as part of the AMOS project at Sourceforge.