ReadDepth

Application data
Biological application domain(s)	Copy number estimation
Maintained?	Maybe
Programming language(s)	R
Licence	Apache License 2.0

Summary: Detects copy number aberrations in deep sequencing data

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Description

ReadDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations.

Links

• ReadDepth Source code [ edit link ]

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References

1. . 2011. PLoS One

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