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CUSHAW

An open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. This aligner is designed based on the well-known seed-and-extend heuristic and has introduced a hybrid seeding approach to improve alignment quality for both SE and PE alignments. This hybrid seeding approach works by incorporating three different seed types, namely MEM seeds, exact-match k-mer seeds and variable-length seeds derived from local alignments.

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CUSHAW forum

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CUSHAW classification

CUSHAW specifications

Software type:
Package/Module
Restrictions to use:
None
Parallelization:
CUDA
Version:
3.0
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable

CUSHAW distribution

versioning

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Credits

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Publications

Institution(s)

Institut für Informatik, Johannes Gutenberg Universität Mainz, Mainz, Germany

Link to literature

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