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rSW-seq

A method for identification of copy number alterations in a tumor genome compared to its matched control, based on application of Smith-Waterman algorithm to single-end sequencing data. In a performance test with simulated data, rSW-seq shows >90% sensitivity and >90% precision in detecting a single copy number change that contains approximately 500 reads for the normal sample. With 100-bp reads, this corresponds to a ~50 kb region for 1X genome coverage of the human genome.

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rSW-seq classification

rSW-seq specifications

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

rSW-seq distribution

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No versioning.

rSW-seq support

Maintainer

  • Peter J. Park <>

Credits

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Publications

Institution(s)

Center for Biomedical Informatics, Harvard Medical School, MA, USA

Link to literature

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