Discover nf-core/viralintegration Open Source project by @nf-core

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Language
Python
License
MIT License
Created over 2 years ago
Updated 7 months ago

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

rnaseq

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

Nextflow

863

sarek

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

Nextflow

388

modules

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

Nextflow

276

tools

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

Python

232

mag

Assembly and binning of metagenomes

Nextflow

210

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

Nextflow

208

chipseq

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

Nextflow

186

atacseq

ATAC-seq peak-calling and QC analysis pipeline

Nextflow

179

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nextflow

179

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

Nextflow

168

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

Nextflow

144

eager

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

Nextflow

141

rnafusion

RNA-seq analysis pipeline for detection of gene-fusions

Nextflow

138

methylseq

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

Nextflow

137

taxprofiler

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

Nextflow

118

viralrecon

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

Nextflow

117

test-datasets

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

100

configs

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

Nextflow

raredisease

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

Nextflow

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

Nextflow

cutandrun

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

Nextflow

smrnaseq

A small-RNA sequencing analysis pipeline

Nextflow

funcscan

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

Nextflow

website

Code and files for the main nf-core website.

Astro

pangenome

Renders a collection of sequences into a pangenome graph.

Nextflow

hlatyping

Precision HLA typing from next-generation sequencing data

Nextflow

bacass

Simple bacterial assembly and annotation pipeline

Nextflow

differentialabundance

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

Nextflow

airrflow

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

Nextflow

bactmap

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

Nextflow

proteinfold

Protein 3D structure prediction pipeline

Nextflow

spatialvi

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

Nextflow

circrna

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

Nextflow

rnasplice

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

Nextflow

demultiplex

Demultiplexing pipeline for sequencing data

Nextflow

epitopeprediction

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

Nextflow

oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Nextflow

rnavar

gatk4 RNA variant calling pipeline

Nextflow

proteomicslfq

Proteomics label-free quantification (LFQ) analysis pipeline

Nextflow

mhcquant

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Nextflow

circdna

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.

Python

isoseq

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

Nextflow

readsimulator

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

Nextflow

scdownstream

A single cell transcriptomics pipeline for QC, integration and making the data presentable

Nextflow

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`).

Nextflow

imcyto

Image Mass Cytometry analysis pipeline

Python

metatdenovo

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

Nextflow

bamtofastq

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

Nextflow

gwas

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

Nextflow

hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Nextflow

fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

Nextflow

clipseq

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

Nextflow

cookiecutter

DEPRECIATED! Please use nf-core/tools instead

Nextflow

kmermaid

k-mer similarity analysis pipeline

Nextflow

dualrnaseq

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

Nextflow

nascent

Nascent Transcription Processing Pipeline

Nextflow

genomeannotator

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

Nextflow

exoseq

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

Nextflow

phaseimpute

Nextflow

metaboigniter

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

Nextflow

genomeassembler

Nextflow

vipr

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

Nextflow

vscode-extensionpack

A VSCode extension pack for nf-core developers.

multiplesequencealign

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

Nextflow

nanostring

An analysis pipeline for Nanostring nCounter expression data.

Nextflow

scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

Nextflow

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.

Nextflow

diaproteomics

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Nextflow

setup-nextflow

A GitHub action to install Nextflow

TypeScript

cageseq

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

Nextflow

pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

HTML

phageannotator

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

Nextflow

mnaseseq

MNase-seq analysis pipeline using BWA and DANPOS2.

Nextflow

coproid

Coprolite host Identification pipeline

Nextflow

molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

Nextflow

variantbenchmarking

A nextflow variant benchmarking pipeline - premature

Nextflow

tfactivity

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

Nextflow

variantcatalogue

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

Nextflow

metapep

From metagenomes to epitopes and beyond

Nextflow

pixelator

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

Nextflow

datasync

nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

Nextflow

phyloplace

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

Groovy

createtaxdb

Parallelised and automated construction of metagenomic classifier databases of different tools

Nextflow

mcmicro

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

Nextflow

createpanelrefs

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

Nextflow

prettier-plugin-nextflow

JavaScript

nf-core.github.io

Now replaced with a new website >>>

Ruby

hicar

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

Nextflow

radseq

Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).

Nextflow

reportho

nf-core pipeline for comparative analysis of ortholog predictions

Nextflow

riboseq

Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

Nextflow

omicsgenetraitassociation

A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis

Nextflow

gh-actions-lint

GitHub Action to run nf-core code linting on a Nextflow pipeline

Shell

crisprvar

[WIP] Evaluate outcomes from genome editing experiments

Nextflow

awsmegatests

CloudFormation templates to setup the aws megatests necessary cloud infrastructure

Shell

marsseq

MARS-seq v2 pre-processing pipeline with velocity

Nextflow

tbanalyzer

An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.

Nextflow

rnadnavar

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

Nextflow

meerpipe

nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis

Nextflow

100

callingcards

A pipeline for processing calling cards data

Nextflow

nf-core/viralintegration

nf-core

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