COMBINE-lab

Resources

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

Showing all resources

seqproc

active

A fast, memory-efficient sequence preprocessing tool with a concise grammar for describing read geometry, matching, and transformations.

Category
Read processing
Language
Rust
Stars
10
Updated
Aug 7, 2026
GitHub
salmon logo

salmon

active

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

Category
Transcriptomics
Language
Rust
Stars
925
Release
v2.5.0
Updated
Aug 10, 2026
bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq
GitHub Docs Release
alevin-fry logo

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
214
Release
v0.16.2
Updated
Jul 10, 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
95
Release
v2.2.0
Updated
Aug 2, 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
67
Release
v0.26.2
Updated
Jul 10, 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
37
Release
v0.21.1
Updated
Jul 10, 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
Jul 29, 2026
GitHub

caps-sa

active
Category
indexing
Language
Rust
Stars
1
Updated
Jun 5, 2026
GitHub

cuttlefish

active

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

Category
de-bruijn Graph
Language
C++
Stars
95
Release
v2.2.0
Updated
Aug 2, 2026
GitHub Release

Transcriptomics

salmon logo

salmon

active

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

Category
Transcriptomics
Language
Rust
Stars
925
Release
v2.5.0
Updated
Aug 10, 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 logo

terminus

maintained

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

Category
Transcriptomics
Language
Rust
Stars
58
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 logo

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
214
Release
v0.16.2
Updated
Jul 10, 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
67
Release
v0.26.2
Updated
Jul 10, 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

Read processing

seqproc

active

A fast, memory-efficient sequence preprocessing tool with a concise grammar for describing read geometry, matching, and transformations.

Category
Read processing
Language
Rust
Stars
10
Updated
Aug 7, 2026
GitHub

Sequence indexing

pufferfish

maintained

An efficient index for colored, compacted de Bruijn graphs.

Category
Sequence indexing
Language
C
Stars
112
Updated
Jun 19, 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
88
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
95
Release
v2.2.0
Updated
Aug 2, 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
Jul 29, 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