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nf-core's Projects

.github icon .github

Files for the @nf-core GitHub organisation

airrflow icon airrflow

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

ampliseq icon ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

atacseq icon atacseq

ATAC-seq peak-calling and QC analysis pipeline

awsmegatests icon awsmegatests

CloudFormation templates to setup the aws megatests necessary cloud infrastructure

bacass icon bacass

Simple bacterial assembly and annotation pipeline

bactmap icon bactmap

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

bamtofastq icon bamtofastq

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

basic_training icon basic_training

Hosts the content of the basic nf-core training on how to create nf-core pipelines with `nf-core create`

cageseq icon cageseq

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

chipseq icon chipseq

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

circdna icon 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.

circrna icon circrna

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

clipseq icon clipseq

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

configs icon configs

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

coproid icon coproid

Coprolite host Identification pipeline

createpanelrefs icon createpanelrefs

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

createtaxdb icon createtaxdb

Parallelised and automated construction of metagenomic classifier databases of different tools

crisprseq icon 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`).

crisprvar icon crisprvar

[WIP] Evaluate outcomes from genome editing experiments

cutandrun icon cutandrun

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

datasync icon datasync

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

deepvariant icon deepvariant

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

denovohybrid icon denovohybrid

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

detaxizer icon 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.

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