Resources

Software and research infrastructure from COMBINE-lab and close collaborators.

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Featured

salmon

active

Efficient, accurate, and bias-aware transcript quantification from RNA-seq data.

Category: Transcriptomics
Language: C++
Stars: 888
Release: v1.11.4
Updated: Mar 11, 2026

bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq

GitHub Docs Release

alevin-fry

active

A suite of tools for processing single-cell sequencing data from RAD files, with a focus on safety, accuracy, speed, and memory efficiency.

Category: Single-cell
Language: Rust
Stars: 207
Release: v0.15.0
Updated: May 20, 2026

10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics

GitHub Docs Release

cuttlefish

active

A fast, parallel, and lightweight tool for constructing compacted de Bruijn graphs from whole-genome references.

Category: de Bruijn graph tools
Language: C++
Stars: 93
Release: v2.2.0
Updated: Feb 26, 2026

GitHub Release

af-anndata

active

alevin-fry related processing of AnnData

Category: Single-Cell
Language: Rust
Stars: 0
Updated: May 20, 2026

GitHub

simpleaf

active

A rust framework to make using alevin-fry even simpler

Category: Single-cell
Language: Rust
Stars: 66
Release: v0.25.0
Updated: May 20, 2026

GitHub Release

piscem-infer

active

Efficient single and multi-sample transcript quantification from mapped RAD-files

Category: Transcriptomics
Language: Rust
Stars: 15
Release: v0.7.0
Updated: May 22, 2026

GitHub Release

piscem

active

Ultrafast and memory-frugal mapping of bulk and single-cell RNA-seq, and single-cell ATAC-seq data

Category: Mapping
Language: Rust
Stars: 33
Release: v0.20.0
Updated: May 7, 2026

GitHub Release

QCatch

active

Convenient and efficient quality control downstream of alevin-fry

Category: Single-cell
Language: Python
Stars: 6
Release: v0.2.11
Updated: Apr 21, 2026

GitHub Release

cf1-rs

active

An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing.

Category: de Bruijn graph tools
Language: Rust
Stars: 1
Updated: May 7, 2026

GitHub

caps-sa

active

Category: indexing
Language: Rust
Stars: 1
Updated: May 27, 2026

GitHub

cuttlefish

active

Building the compacted de Bruijn graph efficiently from references or reads.

Category: de-bruijn Graph
Language: C++
Stars: 93
Release: v2.2.0
Updated: Feb 26, 2026

GitHub Release

Transcriptomics

salmon

active

Efficient, accurate, and bias-aware transcript quantification from RNA-seq data.

Category: Transcriptomics
Language: C++
Stars: 888
Release: v1.11.4
Updated: Mar 11, 2026

bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq

GitHub Docs Release

piscem-infer

active

Efficient single and multi-sample transcript quantification from mapped RAD-files

Category: Transcriptomics
Language: Rust
Stars: 15
Release: v0.7.0
Updated: May 22, 2026

GitHub Release

terminus

maintained

A program for analyzing transcript-level abundance estimates from salmon and collapsing transcripts into robustly estimable groups.

Category: Transcriptomics
Language: Rust
Stars: 56
Release: v0.1.0
Updated: Aug 11, 2022

gene-expression rna-seq transcriptomics

GitHub Release

grouper

maintained

A tool for clustering and annotating contigs from de novo transcriptome assemblies.

Category: Transcriptomics
Language: Python
Stars: 16
Updated: Apr 25, 2019

GitHub

rapmap

legacy

A tool for quasi-mapping and selective alignment of sequencing reads against a transcriptome.

Category: Transcriptomics
Language: C++
Stars: 90
Release: v0.6.0
Updated: Jun 5, 2020

GitHub Release

sailfish

legacy

Rapid alignment-free quantification of isoform abundance.

Category: Transcriptomics
Language: C++
Stars: 127
Release: v0.10.0
Updated: Jun 9, 2022

GitHub Docs Release

Single-cell

alevin-fry

active

A suite of tools for processing single-cell sequencing data from RAD files, with a focus on safety, accuracy, speed, and memory efficiency.

Category: Single-cell
Language: Rust
Stars: 207
Release: v0.15.0
Updated: May 20, 2026

10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics

GitHub Docs Release

simpleaf

active

A rust framework to make using alevin-fry even simpler

Category: Single-cell
Language: Rust
Stars: 66
Release: v0.25.0
Updated: May 20, 2026

GitHub Release

QCatch

active

Convenient and efficient quality control downstream of alevin-fry

Category: Single-cell
Language: Python
Stars: 6
Release: v0.2.11
Updated: Apr 21, 2026

GitHub Release

Sequence indexing

pufferfish

maintained

An efficient index for colored, compacted de Bruijn graphs.

Category: Sequence indexing
Language: C
Stars: 112
Updated: Mar 11, 2026

contigs dbg debruijn debruijn-graph genome hash index

GitHub

mantis

maintained

A fast, compact, and exact large-scale sequence-search index for querying large collections of sequencing experiments.

Category: Sequence indexing
Language: C++
Stars: 87
Updated: Mar 7, 2024

GitHub

squeakr

maintained

A k-mer-counting and multiset-representation system built on the counting quotient filter.

Category: Sequence indexing
Language: C++
Stars: 86
Release: v0.8
Updated: Feb 23, 2025

GitHub Release

de Bruijn graph tools

cuttlefish

active

A fast, parallel, and lightweight tool for constructing compacted de Bruijn graphs from whole-genome references.

Category: de Bruijn graph tools
Language: C++
Stars: 93
Release: v2.2.0
Updated: Feb 26, 2026

GitHub Release

cf1-rs

active

An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing.

Category: de Bruijn graph tools
Language: Rust
Stars: 1
Updated: May 7, 2026

GitHub

deBGR

maintained

A memory-efficient and near-exact representation of the weighted de Bruijn graph using counting-filter data structures.

Category: de Bruijn graph tools
Language: C++
Stars: 31
Updated: Jan 19, 2021

GitHub

rainbowfish

maintained

A succinct data structure for storing and querying colored de Bruijn graphs.

Category: de Bruijn graph tools
Language: C++
Stars: 12
Updated: Sep 11, 2018

GitHub

Other and legacy tools

armatus

legacy

Multiresolution domain-calling software for chromosome conformation capture interaction matrices.

Category: 3D genome organization
Language: C++
Stars: 29
Release: v2.3
Updated: Apr 23, 2025

GitHub Release

matryoshka

legacy

Hierarchical domain-calling software for chromosome conformation capture datasets, based on Armatus.

Category: 3D genome organization
Language: C++
Stars: 7
Release: v0.0.1
Updated: Aug 18, 2017

GitHub Release

GHOST

legacy

A software package for global biological network alignment using spectral signatures to compare topological similarity.

Category: Network biology
Language: Scala
Stars: 0
Updated: Jun 20, 2014

GitHub

growcode

legacy

A non-parametric framework for learning how networks grow.

Category: Legacy
Language: Scala
Stars: 4
Updated: Aug 13, 2013

GitHub

Parana

legacy

A tool for ancestral reconstruction of biological networks.

Category: Legacy
Language: C++
Stars: 2
Updated: Aug 21, 2013

GitHub

rapclust

legacy

A predecessor of Grouper for clustering contigs from de novo transcriptome assemblies.

Category: Legacy
Language: Python
Stars: 31
Updated: Jun 16, 2024

GitHub