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Search results for nf core

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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.

Smrnaseq ⭐ 63

A small-RNA sequencing analysis pipeline

Analysis of Chromosome Conformation Capture data (Hi-C)

Code and files for the main nf-core website.

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

Spatialtranscriptomics ⭐ 34

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

Differentialabundance ⭐ 34

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

Hlatyping ⭐ 34

Precision HLA typing from next-generation sequencing data

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

Proteomicslfq ⭐ 32

Proteomics label-free quantification (LFQ) analysis pipeline

Demultiplex ⭐ 31

Demultiplexing pipeline for sequencing data

Nextflow Gotchas ⭐ 29

A collection of unexpected challenges and learnings with nextflow and nf-core.

Epitopeprediction ⭐ 28

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

Mhcquant ⭐ 28

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Pangenome ⭐ 28

Renders a collection of sequences into a pangenome graph.

Proteinfold ⭐ 26

Protein 3D structure prediction pipeline

gatk4 RNA variant calling pipeline

Mycosnp Nf ⭐ 20

CDCgov/mycosnp-nf

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.

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

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`).

Workflows Nextflow ⭐ 17

Workflow management with Nextflow and nf-core

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.

Metaboigniter ⭐ 11

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

Image Mass Cytometry analysis pipeline

Vscode Extensionpack ⭐ 10

A VSCode extension pack for nf-core developers.

Bamtofastq ⭐ 10

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

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

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

Viralintegration ⭐ 9

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

Readsimulator ⭐ 8

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

k-mer similarity analysis pipeline

Fastquorum ⭐ 8

MNase-seq analysis pipeline using BWA and DANPOS2.

Dualrnaseq ⭐ 7

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

Multiplesequencealign ⭐ 7

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

Phageannotator ⭐ 6

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

Nascent Transcription Processing Pipeline

Configbuilder Nf ⭐ 6

Nextflow config builder scripts for supported HPC infrastructures.

Nanostring ⭐ 6

An analysis pipeline for Nanostring nCounter expression data.

From metagenomes to epitopes and beyond

Nextflow_varcal ⭐ 5

Nextflow Tutorial - Variant Calling Edition

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

Related Searches

Nextflow Nf Core (94)

Pipeline Nf Core (81)

Bioinformatics Nf Core (9)

Sequencing Nf Core (8)

Variant Calling Nf Core (8)

1-72 of 72 search results

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