COMBINE lab

alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

cuttlefish

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

kmers

A bit-packed k-mer representation (and relevant utilities) for rust

oarfish

long read RNA-seq quantification

pufferfish

An efficient index for the colored, compacted, de Bruijn graph

RapMap

Rapid sensitive and accurate read mapping via quasi-mapping

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

simpleaf

A rust framework to make using alevin-fry even simpler

terminus

wasabi

Prepare Sailfish and Salmon output for downstream analysis

COMBINE-lab/salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

COMBINE-lab/alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

COMBINE-lab/pufferfish

An efficient index for the colored, compacted, de Bruijn graph

COMBINE-lab/cuttlefish

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

COMBINE-lab/oarfish

long read RNA-seq quantification

COMBINE-lab/kmers

A bit-packed k-mer representation (and relevant utilities) for rust

COMBINE-lab/simpleaf

A rust framework to make using alevin-fry even simpler

COMBINE-lab/RapClust

Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes

COMBINE-lab/piscem

Rust wrapper for the next generation (still currently in C++)

COMBINE-lab/grangers

COMBINE-lab/pyroe

COMBINE-lab/piscem-infer

COMBINE-lab/combine-lab.github.io

COMBINE-lab/quantaf

COMBINE-lab/piscem-cpp

A small sparse and fast reference index based on SShash and Tiling encoding

COMBINE-lab/sc-census

COMBINE-lab/forseti

COMBINE-lab/lr_quant_benchmarks

A replicable and modular benchmark for long-read RNA transcript quantification methods

COMBINE-lab/TreeTerminus

COMBINE-lab/seqproc

COMBINE-lab/protocol-estuary

COMBINE-lab/roers

COMBINE-lab/libradicl

COMBINE-lab/radtk

Various tools for working with RAD files

COMBINE-lab/rsrs

Reference Signatures (rs) in Rust (rs)

COMBINE-lab/simplr

COMBINE-lab/forseti-experiments

COMBINE-lab/kde-rs

COMBINE-lab/scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

COMBINE-lab/seqcol_rs

(unofficial) Rust implementation of SeqCol sequence collections