Demultiplexing pipeline for sequencing data
☆53Feb 27, 2026Updated this week
Alternatives and similar repositories for demultiplex
Users that are interested in demultiplex are comparing it to the libraries listed below
Sorting:
- Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)☆27Dec 3, 2025Updated 3 months ago
- Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq☆89Updated this week
- Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and gro…☆22Updated this week
- Customer workshop materials☆19May 11, 2023Updated 2 years ago
- Nascent Transcription Processing Pipeline☆22Nov 20, 2025Updated 3 months ago
- Compare the quality of multiple genomes, along with their annotations.☆20Jan 15, 2026Updated last month
- A collection of Groovy classes that provide utility services to nextflow pipelines.☆13Oct 25, 2022Updated 3 years ago
- ☆10Jan 20, 2022Updated 4 years ago
- Pipeline to fetch metadata and raw FastQ files from public databases☆187Feb 8, 2026Updated 3 weeks ago
- A GitHub action to install Nextflow☆26Updated this week
- Classic hello world script in Nextflow language☆23Feb 6, 2026Updated 3 weeks ago
- Simple bacterial assembly and annotation pipeline☆85Feb 23, 2026Updated last week
- Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed …☆49Nov 20, 2025Updated 3 months ago
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.☆13Jun 3, 2025Updated 9 months ago
- Differential gene expression analysis and pathway analysis of RNAseq data☆32Jul 3, 2025Updated 8 months ago
- Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.☆17Jun 3, 2025Updated 9 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- RNA-seq analysis pipeline for detection of gene-fusions☆171Feb 10, 2026Updated 3 weeks ago
- Test data to be used for automated testing with the nf-core pipelines☆150Updated this week
- Nanopore demultiplexing, QC and alignment pipeline☆219Nov 20, 2025Updated 3 months ago
- A pipeline to investigate horizontal gene transfer from NGS data☆26Nov 20, 2025Updated 3 months ago
- A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Remo…☆24Nov 20, 2025Updated 3 months ago
- Nextflow language support for Visual Studio Editor☆37Updated this week
- A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies☆35Jun 30, 2024Updated last year
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆63Nov 20, 2025Updated 3 months ago
- Test data for MultiQC.☆24Feb 21, 2026Updated last week
- Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads☆32Nov 20, 2025Updated 3 months ago
- Luslab nextflow modules☆14Apr 30, 2021Updated 4 years ago
- Python package with helper tools for the nf-core community.☆293Updated this week
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework☆74Updated this week
- Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-dropl…☆313Feb 25, 2026Updated last week
- An analysis pipeline for Nanostring nCounter expression data.☆18Jan 30, 2026Updated last month
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆71Feb 12, 2026Updated 3 weeks ago
- A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted nex…☆57Feb 13, 2026Updated 2 weeks ago
- Experimental plugin to integrate GPT like prompt into Nextflow☆17Apr 15, 2024Updated last year
- A small-RNA sequencing analysis pipeline☆98Jan 7, 2026Updated last month
- rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis☆63Jun 3, 2025Updated 9 months ago