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The Top 23 Pipeline Nf Core Open Source Projects

Open source projects categorized as Pipeline Nf Core
Categories > Nf Core
Categories > Data Processing > Pipeline
Rnaseq ⭐ 718
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
most recent commit 3 months ago
Sarek ⭐ 299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
most recent commit 3 months ago
Tools ⭐ 205
Python package with helper tools for the nf-core community.
dependent packages 2total releases 42most recent commit 3 months agopypi nf-core} Downloads
Modules ⭐ 180
Repository to host tool-specific module files for the Nextflow DSL2 community!
most recent commit 3 months ago
Mag ⭐ 164
Assembly and binning of metagenomes
most recent commit 3 months ago
Atacseq ⭐ 145
ATAC-seq peak-calling and QC analysis pipeline
most recent commit 8 months ago
Chipseq ⭐ 144
ChIP-seq peak-calling, QC and differential analysis pipeline.
most recent commit a year ago
Ampliseq ⭐ 141
Amplicon sequencing analysis workflow using DADA2 and QIIME2
most recent commit 3 months ago
Nanoseq ⭐ 122
Nanopore demultiplexing, QC and alignment pipeline
most recent commit 6 months ago
Methylseq ⭐ 121
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
most recent commit 3 months ago
Rnafusion ⭐ 120
RNA-seq analysis pipeline for detection gene-fusions
most recent commit 4 months ago
Scrnaseq ⭐ 119
A single-cell RNAseq pipeline for 10X genomics data
most recent commit 3 months ago
Eager ⭐ 112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
most recent commit 3 months ago
Viralrecon ⭐ 101
Assembly and intrahost/low-frequency variant calling for viral samples
most recent commit 7 months ago
Fetchngs ⭐ 93
Pipeline to fetch metadata and raw FastQ files from public and private databases
most recent commit 5 months ago
Test Datasets ⭐ 81
Test data to be used for automated testing with the nf-core pipelines
most recent commit 4 months ago
Taxprofiler ⭐ 78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
most recent commit 3 months ago
Configs ⭐ 73
Config files used to define parameters specific to compute environments at different Institutions
most recent commit 3 months ago
Raredisease ⭐ 64
Call and score variants from WGS/WES of rare disease patients.
most recent commit 3 months ago
Hic ⭐ 63
Analysis of Chromosome Conformation Capture data (Hi-C)
most recent commit 5 months ago
Smrnaseq ⭐ 63
A small-RNA sequencing analysis pipeline
most recent commit 3 months ago
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.
most recent commit 4 months ago
Bacass ⭐ 47
Simple bacterial assembly and annotation pipeline
most recent commit 6 months ago
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