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CopySeq specifications

Information


Unique identifier OMICS_00055
Name CopySeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Java, R
Computer skills Advanced
Version 1.7.1
Stability Stable
Maintained No

Versioning


No version available

Documentation


Publication for CopySeq

CopySeq citations

 (2)
library_books

Comparative Studies of Copy Number Variation Detection Methods for Next Generation Sequencing Technologies

2013
PMCID: 3604020
PMID: 23527109
DOI: 10.1371/journal.pone.0059128

[…] excluded because of stability issue. from the same dataset, there were issues getting the code to fully perform to our expectations. our study focused on the method with doc signature, so cnver and copyseq were excluded because they combine both roc and pem signature. a comparison between the combined signature based methods with the single signature based methods can be found in . […]

library_books

Mutational Signatures of De Differentiation in Functional Non Coding Regions of Melanoma Genomes

2012
PMCID: 3415438
PMID: 22912592
DOI: 10.1371/journal.pgen.1002871

[…] about 42% normal cells (). other groups have used similar methods to estimate tumor sample purity ., we first estimate copy number in non-overlapping 5 kb tiles in the normal genome using the copyseq algorithm . we only consider tiles with 80% uniquely mappable k-mers (which is 94% of the tiles) to ensure accurate copy number estimation. to detect amplifications and deletions […]


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CopySeq institution(s)
Department of Molecular Genetics, Crown Human Genome Center, Weizmann Institute of Science, Rehovot, Israel

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