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CloudBrush

Detects structural defects by examining the neighboring reads of a specific read for sequencing errors and adjusting the edges of the string graph. CloudBrush is a conservative assembler that nevertheless can generate precise contigs that avoid error propagation in downstream analysis with moderate N50 contig lengths. It can be implemented as a modular pipeline, allowing to be easily extended when improved algorithms have been developed.

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CloudBrush classification

CloudBrush specifications

Software type:
Framework/Library
Restrictions to use:
None
Parallelization:
MapReduce
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
High performance computing:
Yes

CloudBrush distribution

versioning

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CloudBrush forum

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CloudBrush classification

CloudBrush specifications

Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Java
Computer skills:
Advanced
Interface:
Command line interface
Operating system:
Unix/Linux
License:
Other
Stability:
Stable

CloudBrush distribution

versioning

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CloudBrush support

Documentation

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Publications

Institution(s)

Institute of Information Science, Academia Sinica, Taipei, Taiwan, China; Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, China

Funding source(s)

Supported by National Science Council grant NSC 99-2321-B-001-025.

Link to literature

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