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.