Discover COMBINE-lab/SalmonTools Open Source project

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

735

alevin-fry

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

141

pufferfish

105

RapMap

Rapid sensitive and accurate read mapping via quasi-mapping

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

cuttlefish

terminus

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

kmers

long read RNA-seq quantification

oarfish

Prepare Sailfish and Salmon output for downstream analysis

wasabi

simpleaf

A rust framework to make using alevin-fry even simpler

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

RapClust

Improved multi-sample transcript abundance estimates using adaptive priors

shoal

grangers

pufferfish2

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

EDS

pyroe

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

piscem

piscem-infer

A Rust library for building modular, fast and compact indexes over genomic data

mazu

grouper

A succinct colored dBG representation

rainbowfish

semi-reference-based short read compression

quark

Useful scripts and tools related to alevin-fry

usefulaf

minnow

A treatise on quantification and differential expression from RNA-seq data

measuresmatter

combine-lab.github.io

HTML

quantaf

Nextflow

seine-rs

A (rust)🦀 library and suite of tools for manipulating and processing the output of salmon, alevin, and alevin-fry 🐟

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

piscem-cpp

GRASS

Graph-Regularized Annotation via Semi-Supervised learning

Methods for the automated discovery of hierarchically-structured chromatin domains

TreeTerminus

matryoshka

A simple pipeline using CGAT framework for benchmarking and analysis.

alevin-paper-pipeline

A crate to convert "complex" sequence library geometries to "simple" geometries

seq_geom_xform

COMBINE-lab.github.io-OLD

Lab website

HTML

seqproc

A small "lightweight" implementation of PCA in C++ using the Eigen library

pcalib

perplexity

Testing out rust parsing of single-cell library geometry specifications

seq_geom_parser

Specification for the extended fragment geometry description language

roe

efgdl-spec

protocol-estuary

Jsonnet

A GitHub clone of the XZ repo (http://git.tukaani.org/xz.git) — not from the original author

LabRules

A list of rules and hints (on various different subjects) for members of the COMBINE lab. Others may also find them useful.

txome-clustering

Meaningful and efficient clustering of de novo transcriptome assembly results (better name pending).

Super fast C++ logging library.

spdlog

roers

An attempt at rustification of the CQF (https://github.com/splatlab/cqf)

cqf-rust

libgff

splitp

split-seq preprocessing

forseti

quant-tx-diversity

alevin-fry-paper-scripts

scrna-ambiguity

This is a support website for Alevin-tool (part of Salmon).

alevin-tutorial

radicl-cpp

Internal library for basic reading and writing of .rad files in C++14

Get the "signature" of fasta files

FastaDigest

Documenting the (binary) output format used by Kallisto

KallistoFormatDescription

pufferfish_experiments

CSE549-txpCoverage

QuantAnalysis