demultiplexing

There are 1 repository under demultiplexing topic.

• nf-core / nanoseq

  Nanopore demultiplexing, QC and alignment pipeline

  alignmentdemultiplexingnanoporenextflownf-corepipelineqcworkflow
  Language:Nextflow 143
• barcoding

  PacificBiosciences / barcoding

  Lima - Demultiplex Barcoded PacBio Samples

  single-moleculebarcodedemultiplexinglimapacbio
  Language:R 62

• clintval / sample-sheet

  Parse Illumina sample sheets with Python

  illuminabioinformaticsdemultiplexingsamplesheetexperiment-managerpython
  Language:Python 47

• grenaud / deML

  Maximum likelihood demultiplexing

  c-plus-plusdemultiplexingmaximum-likelihoodsequencing
  Language:C++ 45

• nf-core / demultiplex

  Demultiplexing pipeline for sequencing data

  nf-corenextflowworkflowdemultiplexingilluminabcl2fastqpipelinebases2fastqelementbiosciences
  Language:Nextflow 34

• gaolabtools / scNanoGPS

  Single cell Nanopore sequencing data for Genotype and Phenotype

  cell-barcodedemultiplexinggene-expressionisoformslong-read-sequencingnanopore-analysis-pipelinerna-seq-pipelinesingle-cellsingle-nucleotide-variationumi-curation
  Language:Python 32

• OpenGene / defq

  Please switch to https://github.com/OpenGene/defastq

  fastqdemultiplexingsplitindexilluminadual-indexsequencingdemux
  Language:C 27

• paulranum11 / SPLiT-Seq_demultiplexing

  An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

  scrna-seqscrna-seq-analysissplit-seqfastqdemultiplexingsingle-cellsingle-cell-rna-seqsingle-cell-analysissingle-cell-omicssingle-cell-sequencing
  Language:Python 25

• biosails / pheniqs

  Fast and accurate sequence demultiplexing

  sequencingmultiplexingdemultiplexingbamcramsamfastqbarcodetagtaggingclassifiersautocompleterobust
  Language:C++ 23
• demuxalot

  arogozhnikov / demuxalot

  Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

  biotechdemultiplexingscrnaseqsingle-cell-analysis
  Language:Python 20

• theislab / hadge

  Comprehensive pipeline for donor demultiplexing in single cell

  deconvolutiondemultiplexingsingle-cell
  Language:Nextflow 19

• fairliereese / LR-splitpipe

  Demultiplexing and debarcoding tool designed for LR-Split-seq data.

  single-celllong-readtranscriptomerna-seqdemultiplexing
  Language:Python 16

• bihealth / digestiflow-server

  :cocktail: Web-based database system for flow cell management (incl. REST API)

  bioinformaticsilluminademultiplexing
  Language:Python 15

• Ebedthan / sabreur

  fast, reliable and handy demultiplexing tool for fastx files

  bioinformaticsdemultiplexingrustsequence-analysis
  Language:Rust 14

• Gartner-Lab / deMULTIplex2

  deMULTIplex2: robust sample demultiplexing for scRNA-seq

  bioinformatics-algorithmsdemultiplexingscrna-seqstatistical-modelsmulti-seqcell-hashing
  Language:R 8

• bihealth / flowcelltool

  Simple management of Illumina sequencing flowcells

  bioinformaticssequencingdemultiplexing
  Language:Python 7

• vibaotram / baseDmux

  snakemake workflow for basecalling and demultiplexing of ONT sequencing data

  snakemake-workflowbasecallingdemultiplexingnanopore
  Language:Python 5

• bihealth / cubi_demux

  Demultiplexing utility, companion to flowcelltool.

  bioinformaticsilluminademultiplexing
  Language:Python 4

• bixBeta / CFG

  RNA-seq workflow for UALBANY CFG - Demux, QC, Vis, Align, preProcess, DGE Calls

  illuminademultiplexingbcl2fastqfastqcmultiqcstaralignmenthomer
  Language:R 4

• NYU-Molecular-Pathology / demux-nf

  Nextflow pipeline for Illumina NGS demultiplexing

  nextflowpipelinedemultiplexingbcl2fastq
  Language:Nextflow 3

• ryandkuster / ngsComposer

  Base-call error-filtering and read preprocessing pipeline for fastq libraries

  genomebioinformaticsdata-visualizationdata-filteringilluminafastqtrimmingdemultiplexingqc
  Language:Python 3

• sagc-bioinformatics / mgikit

  mgikit is a collection of tools used to demultiplex fastq files and generate demultiplexing and quality reports.

  demultiplexingfastqmgi
  Language:Rust 3

• bihealth / digestiflow-demux

  :spaghetti: Digestiflow Demultiplexing Tool

  bioinformaticsdemultiplexingillumina
  Language:Python 2

• bodeolukolu / ngsComposer

  demultiplexingngsquality-filteringadapter-removalvariable-length-barcodeerror-detectionbarcode-swappingempirical-quality-filteringindex-hopping
  Language:C++ 2

• Grelot / seaConnect--dDocent

  GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

  gbsgenomicsvariant-callingradseqddocentstacksingularitysnakemakedemultiplexingsnpgenotypingsingularity-recipevcffastqpopulation-geneticsbioinformatics
  Language:Shell 2

• jenzopr / pydemult

  :fast_forward: Streamed and parallel demultiplexing of fastq files in python

  fastqbarcodedemultiplexing
  Language:Python 2

• AstraBert / RREQUESTED

  RREQUESTED: A versatile shellscript tool based on Python scripts to preprocess raw basecalled reads with quality and size filtering and ex-novo demultiplexing

  bioinformaticsdemultiplexingeasy-to-usegenomicsbeginner-friendlycondanext-generation-sequencingoxford-nanopore
  Language:Python 1

• AstraBert / rrequested-demultiplex

  rrequested-demultiplex (Raw REads QUality Extraction, Size Trimming and Ex-novo Demultiplexing) is a python package aimed at preprocessing (quality filtering, size selection and demultiplexing) raw basecalled reads, especially produced by Oxford Nanopore, a Third Generation Sequencing technology.

  data-manipulationdemultiplexinggenomicsoxford-nanoporepythonpython-packagesequencing
  Language:Python 1

• bihealth / digestiflow-cli

  :spaghetti: Digestiflow Command Line Client

  bioinformaticsdemultiplexingillumina
  Language:Rust 1

• Dadido3 / mxv-demuxer

  Tool to demux/unpack mxv (MAGIX video) files

  demultiplexingdemuxdemuxervideo-container
  Language:Go 1

• lipkau / Spread

  This module implements helper functions that allow you to set parameters to a context. The parameters provided will be spread across the commands in the context.

  powershellmoduledemultiplexingdemuxspread
  Language:PowerShell 1

• marlaux / Metabarcoding-script-by-script

  Former version of METAPIPE

  demultiplexingmetabarcodingotu-tablephyloseqpipelinetaxonomy-assignmentworkflow
  Language:Shell 1
• anglerfish

  remiolsen / anglerfish

  Anglerfish - Nanopore reads from Illumina libraries

  demultiplexingnanopore
  Language:Python 1

• brettwhitty / GoBCLy

  POC code for specific streaming demultiplexing applications; contact author for more details.

  bioinformaticsdemultiplexingfastqgolang
  Language:Go 0

• Chris-Anthony / demultiplexing-Chris-Anthony

  custom python script to demultiplex sequencing reads

  demultiplexing
  Language:Python 0

• AndriyKalashnykov / go-demux

  a simple de-multiplexer in golang

  demultiplexingdemuxdemuxergogolang
  Language:Go