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Search results for pipeline nf core

64 search results found

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Python package with helper tools for the nf-core community.

Modules ⭐ 180

Repository to host tool-specific module files for the Nextflow DSL2 community!

Assembly and binning of metagenomes

Atacseq ⭐ 145

ATAC-seq peak-calling and QC analysis pipeline

Chipseq ⭐ 144

ChIP-seq peak-calling, QC and differential analysis pipeline.

Ampliseq ⭐ 141

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nanoseq ⭐ 122

Nanopore demultiplexing, QC and alignment pipeline

Methylseq ⭐ 121

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Rnafusion ⭐ 120

RNA-seq analysis pipeline for detection gene-fusions

Scrnaseq ⭐ 119

A single-cell RNAseq pipeline for 10X genomics data

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Viralrecon ⭐ 101

Assembly and intrahost/low-frequency variant calling for viral samples

Fetchngs ⭐ 93

Pipeline to fetch metadata and raw FastQ files from public and private databases

Test Datasets ⭐ 81

Test data to be used for automated testing with the nf-core pipelines

Taxprofiler ⭐ 78

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Config files used to define parameters specific to compute environments at different Institutions

Raredisease ⭐ 64

Call and score variants from WGS/WES of rare disease patients.

Analysis of Chromosome Conformation Capture data (Hi-C)

Smrnaseq ⭐ 63

A small-RNA sequencing analysis pipeline

Cutandrun ⭐ 54

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Simple bacterial assembly and annotation pipeline

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Airrflow ⭐ 40

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

Deepvariant ⭐ 38

Google's DeepVariant variant caller as a Nextflow pipeline

Differentialabundance ⭐ 34

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Hlatyping ⭐ 34

Precision HLA typing from next-generation sequencing data

Proteomicslfq ⭐ 32

Proteomics label-free quantification (LFQ) analysis pipeline

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Demultiplex ⭐ 31

Demultiplexing pipeline for sequencing data

Mhcquant ⭐ 28

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Epitopeprediction ⭐ 28

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

Pangenome ⭐ 28

Renders a collection of sequences into a pangenome graph.

Proteinfold ⭐ 26

Protein 3D structure prediction pipeline

gatk4 RNA variant calling pipeline

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Rnasplice ⭐ 18

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

Crisprseq ⭐ 17

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

A pipeline to investigate horizontal gene transfer from NGS data

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

Genomeassembler ⭐ 12

Genomeannotator ⭐ 11

Pipeline for the identification of (coding) gene structures in draft genomes.

Image Mass Cytometry analysis pipeline

Metaboigniter ⭐ 11

Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

Assembly and intrahost / low-frequency variant calling for viral samples

Please consider using/contributing to https://github.com/nf-core/sarek

Bamtofastq ⭐ 10

Converts bam or cram files to fastq format and does quality control.

Viralintegration ⭐ 9

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

k-mer similarity analysis pipeline

Fastquorum ⭐ 8

Readsimulator ⭐ 8

A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.

Multiplesequencealign ⭐ 7

A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

Dualrnaseq ⭐ 7

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

MNase-seq analysis pipeline using BWA and DANPOS2.

Nascent Transcription Processing Pipeline

Nanostring ⭐ 6

An analysis pipeline for Nanostring nCounter expression data.

Configbuilder Nf ⭐ 6

Nextflow config builder scripts for supported HPC infrastructures.

Phageannotator ⭐ 6

Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.

From metagenomes to epitopes and beyond

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

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