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
4
Updated
Jul 13, 2026
GitHub
salmon logo

salmon

active

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

Category
Transcriptomics
Language
Rust
Stars
920
Release
v2.3.4
Updated
Jul 25, 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
213
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
Jul 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
v0.26.2
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
Jun 19, 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
Jul 26, 2026
GitHub Release

Transcriptomics

salmon logo

salmon

active

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

Category
Transcriptomics
Language
Rust
Stars
920
Release
v2.3.4
Updated
Jul 25, 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
57
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
213
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
66
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
4
Updated
Jul 13, 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
Jul 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
Jun 19, 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