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Search results for nextflow nf core
nextflow
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nf-core
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72 search results found
Rnaseq
⭐
718
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Tools
⭐
205
Python package with helper tools for the nf-core community.
Modules
⭐
180
Repository to host tool-specific module files for the Nextflow DSL2 community!
Mag
⭐
164
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
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141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Nanoseq
⭐
122
Nanopore demultiplexing, QC and alignment pipeline
Methylseq
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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
Eager
⭐
112
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
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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
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Configs
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73
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
Hic
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63
Analysis of Chromosome Conformation Capture data (Hi-C)
Website
⭐
58
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.
Bacass
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47
Simple bacterial assembly and annotation pipeline
Bactmap
⭐
45
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
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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
⭐
32
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
Rnavar
⭐
23
gatk4 RNA variant calling pipeline
Mycosnp Nf
⭐
20
CDCgov/mycosnp-nf
Lncpipe
⭐
18
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
Circdna
⭐
18
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.
Quantms
⭐
17
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
Hgtseq
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17
A pipeline to investigate horizontal gene transfer from NGS data
Clipseq
⭐
14
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
Isoseq
⭐
14
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
Gwas
⭐
12
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
Genomeassembler
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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.
Imcyto
⭐
11
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.
Exoseq
⭐
10
Please consider using/contributing to https://github.com/nf-core/sarek
Vipr
⭐
10
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.
Kmermaid
⭐
8
k-mer similarity analysis pipeline
Fastquorum
⭐
8
Mnaseseq
⭐
7
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
⭐
6
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.
Metapep
⭐
6
From metagenomes to epitopes and beyond
Nextflow_varcal
⭐
5
Nextflow Tutorial - Variant Calling Edition
Cageseq
⭐
5
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
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1-72 of 72 search results
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