Turakhia Lab

Tools

metaWEPP

metaWEPP is a computational framework for haplotype-level analysis of all pathogens present in metagenomic sequencing data.

DIPPER

DIPPER is an ultrafast, distance-based phylogenetic tool that utilizes GPU acceleration to reconstruct ultralarge phylogenies through divide-and-conquer and placement techniques.

WEPP

WEPP is a pathogen-agnostic tool for haplotype-level analysis of wastewater sequencing data.

TWILIGHT

TWILIGHT is an alignment tool designed for ultrafast and ultralarge multiple sequence alignment, with support for GPU acceleration.

DP-HLS

DP-HLS is an HLS-based framework to accelerate the implementation of 2-D DP kernels, widely used in bioinformatics, on FPGA.

ROADIES

ROADIES is a fully-automated pipeline designed for species tree inference directly from their raw genomic assemblies.

PanMAN

PanMAN or Pangenome Mutation-Annotated Network is a novel data representation for pangenomes that provides massive leaps in both representative power and storage efficiency.

TALCO

TALCO is a novel method for tiling genome sequence alignments by leveraging convergence of traceback pointers that allows it to maintain a constant memory footprint during the acceleration step independent of alignment length while also ensuring optimal alignments under banding constraints.

RIVET

RIVET is a software pipeline and visual web platform to perform SARS-CoV-2 recombination inference.

UShER

UShER is a package consisting of a family of programs (UShER, matOptimize, matUtils, RIPPLES) for rapid phylogenetic and recombination analyses, particularly suitable for the SARS-CoV-2 genomes.