The following software is primarily developed or maintained by the COMBINE-lab or by members of the COMBINE-lab in conjunction with others.
salmon is a tool for efficient, accurate, and bias-aware transcript quantification from RNA-seq data
alevin-fry is a suite of tools for processing single-cell sequencing data. It consumes RAD files generated by alevin, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell. The focus in alevin-fry is on safety, accuracy and efficiency (in terms of both time and memory usage).
Pufferfish An efficient index for the colored, compacted, de Bruijn graph
A fast, compact, and exact large-scale sequence-search index. Mantis is a data structure for indexing and querying hundreds, thousands or tens of thousands (or more) sequencing experiments for the likely presense of a query string.
Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from whole genome reference(s).
Terminus is a program for analyzing transcript-level abundance estimates from RNA-seq data, computed using salmon, and collapsing individual transcripts into groups whose total transcriptional output can be estimated more accurately and robustly.
deBGR a memory-efficient and near-exact representation of the weighted de Bruijn Graph. Our representation is based upon a recently-introduced counting filter data structure which, itself, provides an approximate representation of the weighted de Bruijn Graph.
Squeakr is a k-mer-counting and multiset-representation system using the recently-introduced counting quotient filter (CQF) Pandey et al. (2017), a feature-rich approximate membership query (AMQ) data structure.
Rainbow fish is succinct data structure to store and query colored DBG.
Grouper is a tool for clustering and annotating contigs from de novo transcriptome assemblies.
RapMap is a tool for quasi-mapping and selective alignment of sequencing reads against a transcriptome.
Rapid alignment-free quantification of isoform abundance.
GHOST is a software package for global biological network alignment. It computes alignments based on a novel spectral signature for comparing the topological similarity of nodes across networks.
Multiresolution domain calling software for chromosome conformation capture interaction matrices.
Hierarchical domain calling software for chromosome conformation capture datasets. Basad on the multiresolution domain calling tool, Armatus. (http://www.cs.cmu.edu/~ckingsf/software/armatus/).