nf-core

nf-core

Geek Repo

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Home Page:http://nf-co.re

Twitter:@nf_core

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nf-core's repositories

modules

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

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tools

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

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mag

Assembly and binning of metagenomes

Language:NextflowLicense:MITStargazers:179Issues:136Issues:244

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Language:NextflowLicense:MITStargazers:155Issues:148Issues:312

eager

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

Language:NextflowLicense:MITStargazers:122Issues:155Issues:418

taxprofiler

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

Language:NextflowLicense:MITStargazers:87Issues:147Issues:176

test-datasets

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

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

Language:NextflowLicense:MITStargazers:73Issues:116Issues:89

website

Code and files for the main nf-core website.

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funcscan

(Meta-)genome screening for functional and natural product gene sequences

Language:NextflowLicense:MITStargazers:53Issues:71Issues:124

bacass

Simple bacterial assembly and annotation pipeline

Language:NextflowLicense:MITStargazers:50Issues:144Issues:45

differentialabundance

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

Language:NextflowLicense:MITStargazers:40Issues:131Issues:100

demultiplex

Demultiplexing pipeline for sequencing data

Language:NextflowLicense:MITStargazers:32Issues:68Issues:68

epitopeprediction

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

Language:NextflowLicense:MITStargazers:32Issues:113Issues:68

mhcquant

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Language:NextflowLicense:MITStargazers:29Issues:61Issues:76

crisprseq

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`).

Language:NextflowLicense:MITStargazers:19Issues:123Issues:20

readsimulator

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

Language:NextflowLicense:MITStargazers:15Issues:0Issues:0

oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Language:NextflowLicense:MITStargazers:12Issues:184Issues:5

vscode-extensionpack

A VSCode extension pack for nf-core developers.

setup-nextflow

A GitHub action to install Nextflow

Language:TypeScriptLicense:MITStargazers:9Issues:146Issues:12
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detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

Language:NextflowLicense:MITStargazers:7Issues:0Issues:0

phageannotator

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

Language:NextflowLicense:MITStargazers:7Issues:139Issues:60

metapep

From metagenomes to epitopes and beyond

Language:PythonLicense:MITStargazers:6Issues:16Issues:20

tfactivity

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

Language:NextflowLicense:MITStargazers:5Issues:0Issues:0

createpanelrefs

Generate Panel of Normals, models or other similar references from lots of samples

Language:NextflowLicense:MITStargazers:4Issues:0Issues:0

mcmicro

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

Language:NextflowLicense:MITStargazers:4Issues:171Issues:0

pixelator

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

Language:NextflowLicense:MITStargazers:4Issues:0Issues:0

createtaxdb

Parallelised and automated construction of metagenomic classifier databases of different tools

Language:NextflowLicense:MITStargazers:3Issues:183Issues:22
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