:: DESCRIPTION
ConPADE is a tool used to estimate contig ploidy and allele dosage in polyploid genome assemblies.
::DEVELOPER
Microsoft Computational Biology Tools
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Margarido GR, Heckerman D.
ConPADE: genome assembly ploidy estimation from next-generation sequencing data.
PLoS Comput Biol. 2015 Apr 16;11(4):e1004229. doi: 10.1371/journal.pcbi.1004229. PMID: 25880203; PMCID: PMC4400156.
:: DESCRIPTION
EXPANDS characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Andor, N., Harness, J. V., Müller, S., Mewes, H. W. & Petritsch, C.
EXPANDS: expanding ploidy and allele frequency on nested subpopulations.
Bioinforma. Oxf. Engl. 30, 50–60 (2014).
:: DESCRIPTION
The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.
HAPSEG is a probabilistic method to interpret bi- allelic marker data in cancer samples.
::DEVELOPER
The Cancer Genome Analysis (CGA) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Scott L Carter, et cl.
Absolute quantification of somatic DNA alterations in human cancer
Nature Biotechnology 30, 413–421 (2012) doi:10.1038/nbt.2203
Scott L. Carter, Matthew Meyerson & Gad Getz
Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping
