Kmer Analysis of Pileups for Genotyping

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Structural variant toolkit for VCFs

A variant caller for the GBA gene using WGS data

Kmer based genotyper for short reads.

STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford…

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes

A tool set to assess the quality of the per read phasing and reduce the errors.

Script that takes samtools pileup output and write consensus fasta file as output.

A simple framework to simulate parental and admixture offsprings. The framework allows for a benchmark to distinguish inheritance blocks on the offsprings.

ROBust INference of admixture time

Graph realignment tools for structural variants

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Method to optimally select samples for validation and resequencing

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

Structural Variant Index

10x Genomics Reads Simulator

Code for phasing SVs with SNPs

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)