Project Software

This page contains information about software written by me or the students in my group, or to which we have contributed.

Pufferfish

Pufferfish An efficient index for the colored, compacted, de Bruijn graph

Mantis

Mantis A Fast, Small, and Exact Large-Scale Sequence-Search Index

deBGR

deBGR An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph

Squeakr

Squeakr An exact and approximate k-mer counting system based on the counting quotient filter

Rainbowfish

Rainbowfish A succinct representation of colored de Bruijn graphs

Grouper

Grouper Analysis and annotation of de novo transcriptomes (the successor to RapClust)

RapClust

RapClust Accurate, lightweight clustering of de novo transcriptomes using fragment equivalence classes

RapClust

RapClust Accurate, lightweight clustering of de novo transcriptomes using fragment equivalence classes

Matryoshka

Matryoshka Automated discovery of hierarchically-structured chromatin domains

Salmon

Salmon another tool for rapid, bias-aware, quantification from RNA-seq

RapMap

RapMap Rapid sensitive and accurate transcriptome analysis via quasi-mapping

Sailfish

Sailfish is a tool for the rapid, alignment-free quantification of transcripts from RNA-seq

GHOST

GHOST is a biological network alignment package

GrowCode

GrowCode is software to automatically learn a model of growth underpinning a network.

PARANA

PARANA is software to infer the interaction history of biological networks.

Starfish

Starfish is software to analyze graph rigidity.

Other Software

This is other software (e.g. libraries, tools) that I've written or to which I've contributed that are not directly assoicated with any projects or publications

SlimGraph

SlimGraph is a small (the library is small, not the graphs it handles) graph library for Scala. It's meant to be simple and fast.

MCFlow

MCFlow is a C++ implementation of mean curvature flow for 3D meshes using backward-euler integration to minimize instabilities in the flow.

AtlasGen

AtlasGen is a Python script I wrote to help easily generate texture atlases.

EigenTools

EigenTools is a set of wrapper classes I wrote for the Slepc eigensolver to ease the syntactic and semantic burden of computing large eigendecompositions in C++ (note: Google seems to currently have some trouble fetching the actual code. I have a backup, and I'll probably be moving this project to GitHub soon anyway.)