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Acacia

An error-corrector for pyrosequenced amplicon reads. Acacia reduces the number and complexity of alignments. Rather than performing all-against-all alignments in a cluster, each read in the cluster is aligned to a dynamically updated cluster consensus; the alignment algorithm is made more efficient using heuristics that only consider homopolymer over and under-calls. Acacia uses a quicker but less sensitive statistical approach to distinguish between error and genuine sequence differences. Acacia is an alternative to AmpliconNoise and Denoiser that maintains sensitivity without compromising genuine signal in the data.

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Acacia classification

Acacia specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Biological technology:
Roche
Programming languages:
Java
Stability:
Stable

Acacia distribution

versioning

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No versioning.

Acacia support

Documentation

Maintainer

  • Gene W. Tyson <>

Credits

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Publications

Institution(s)

Advanced Water Management Centre, The University of Queensland, St. Lucia, QLD, Australia; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia; Commonwealth Scientific and Industrial Research Organisation Mathematics, Informatics and Statistics, QLD, Australia; School of Computing and Mathematics, University of Western Sydney, NSW, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia

Funding source(s)

This project was supported by a PhD scholarship funded by the Commonwealth Scientific and Industrial Research Organisation Transformational Biology capability platform, by a Queen Elizabeth II Fellowship from the Australian Research Council (grant No. DP1093175) and by a strategic University of Queensland funding of the Australian Centre for Ecogenomics.

Link to literature

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