Episomizer – Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data

Episomizer

:: DESCRIPTION

Episomizer is currently a semi-automatic computational pipeline to construct circular DNA structures through identifying SVs connecting the boundaries of highly amplified CNA segments followed by a graph theoretical algorithm that searches for cyclic graphs.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R
  • Python

:: DOWNLOAD

Episomizer

:: MORE INFORMATION

Citation

Xu K, Ding L, Chang TC, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G.
Structure and evolution of double minutes in diagnosis and relapse brain tumors.
Acta Neuropathol. 2019 Jan;137(1):123-137. doi: 10.1007/s00401-018-1912-1.

HMMcopy 0.1.1 – HMM for Detecting Somatic Copy Number alterations in tumour-normal paired Whole Genome Sequencing data

HMMcopy 0.1.1

:: DESCRIPTION

HMMcopy is a suite of tools to make copy number estimations for whole genome data with GC and mappability correction, then segment and classify copy number profiles with a robust Hidden Markov Model. Designed to work with high coverage whole genome HTS data, it can derive copy number estimations from large (~250GB) aligned BAM files in 2 hours on a single core with minimal memory requirements.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

 HMMcopy

:: MORE INFORMATION

Citation

G. Ha, A. Roth, D. Lai, A. Bashashati, J. Ding, R. Goya, R. Giuliany, J. Rosner, A. Oloumi, K. Shumansky, S.-F. Chin, G. Turashvili, M. Hirst, C. Caldas, M. A. Marra, S. Aparicio, S. P. Shah.
Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer.
Genome Research 2012 Oct;22(10):1995-2007.

VarGeno v1.0.3 – SNP Genotyping from Whole Genome Sequencing data

VarGeno v1.0.3

:: DESCRIPTION

VarGeno is a method for SNP genotyping from Illumina whole genome sequencing data. VarGeno builds upon LAVA by improving the speed of k-mer querying as well as the accuracy of the genotyping strategy.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VarGeno

:: MORE INFORMATION

Citation:

Bioinformatics, 35 (3), 415-420 2019 Feb 1
Toward Fast and Accurate SNP Genotyping From Whole Genome Sequencing Data for Bedside Diagnostics
Chen Sun , Paul Medvedev

PhyloWGS 1.0-rc2 – Inferring Subclonal Composition and Evolution from Whole-genome Sequencing data

PhyloWGS 1.0-rc2

:: DESCRIPTION

PhyloWGS can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations.

::DEVELOPER

Morris Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python

:: DOWNLOAD

  PhyloWGS

:: MORE INFORMATION

Citation

Genome Biol. 2015 Feb 13;16(1):35. doi: 10.1186/s13059-015-0602-8.
PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q.