Software
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A novel method for detecting and genotyping somatic structural variations (SVs) and building phylogenetic trees in multiple whole-genome sequencing tumor samples.
The CNN_Smoothie pipeline presented here provides a framework that can be easily implemented for many different applications, including immunohistochemistry grading and detecting tumor subtypes and biomarkers.
A graph-based method for deconvolution of 10X Genomics Linked-Reads. A more efficient multi-threaded version of this software is currently being developed. This program was used to write our manuscript 'Minerva: An Alignment and Reference Free Approach to Deconvole Linked-Reads for Metagenomics'
Novel-X detects and genotypes novel sequence insertions in 10X sequencing dataset using non-trivial read alignment signatures and barocde information.
Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations. We introduced and implemented the Dollo(k) phylogeny model for this problem.
BAyesian Model SElection for Inferring the subclonal history of tumor samples.
Selected software developed before the official inception of the lab
VariationHunter/CommonLAW (integrated in Tardis)
A tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.
The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
An efficient deterministic algorithm which directly maximizes the similarity between two labeled gene trees and finds interaction partners among protein/domain families.
Uses Alon et al's color coding technique for counting non-induced occurrences of subgraph topologies in the form of trees.
Binary Tree Partition (BTP) is a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations.