AsymTools specifications

Information


Unique identifier OMICS_29566
Name AsymTools
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A list of mutations for each cohort of whole-genome sequencing somatic variants.
Output data A map compiling asymmetries detected in each cohort.
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability No
Registration required Yes
Maintained No

Versioning


No version available

Maintainers


This tool is not available anymore.

Publication for AsymTools

AsymTools citations

 (2)
library_books

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus Associated Merkel Cell Carcinoma

2017
MBio
PMCID: 5210499
PMID: 28049147
DOI: 10.1128/mBio.02079-16

[…] mutation signatures from the somatic mutations of each tumor genome. To determine mutation strand asymmetries and produce subsequent plots, we input somatic mutations grouped by MCPyV status into the AsymTools Matlab script ().Mutation clusters (kataegis) were evaluated by taking the distance in base pairs from one somatic single-base substitution to the previous mutation or intermutational distan […]

library_books

Mutation Processes in 293 Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B

2016
PLoS One
PMCID: 4862684
PMID: 27163364
DOI: 10.1371/journal.pone.0155391

[…] e using nsNMF decomposition instead of Brunet NMF decomposition as described by Covington and colleagues []. Mutation strand asymmetries were analyzed using somatic mutations from all samples and the AsymTools MatLab software []. All raw sequences are available from NCBI SRA under project number, PRJNA312357. […]

AsymTools institution(s)
Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Carnegie Mellon University School of Computer Science, Pittsburgh, PA, USA; Baylor College of Medicine, Houston, TX, USA; Stanford University Department of Biology, Stanford, CA, USA; Cornell University Department of Molecular Biology and Genetics, Ithaca, NY, USA

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