16 nf-core/mhcquant

mass-spectrometry mhc openms peptides proteomics

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Version 2.1.0   Published 5 hours ago

46 nf-core/fetchngs

ddbj download ena fastq geo sra synapse

Pipeline to fetch metadata and raw FastQ files from public and private databases

Version 1.5   Published 1 week ago

61 nf-core/eager

adna ancient-dna-analysis ancientdna genome metagenomics pathogen-genomics population-genetics

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

Version 2.4.1   Published 1 week ago

56 nf-core/nanoseq

alignment demultiplexing nanopore qc

Nanopore demultiplexing, QC and alignment pipeline

Version 2.0.1   Published 1 week ago

69 nf-core/mag

annotation assembly binning long-read-sequencing metagenomes metagenomics nanopore nanopore-sequencing

Assembly and binning of metagenomes

Version 2.1.1   Published 2 weeks ago

17 nf-core/cutandrun

cutandrun cutandrun-seq cutandtag cutandtag-seq

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

Version 1.0.0   Published 1 month ago

75 nf-core/ampliseq

16s amplicon-sequencing metagenomics qiime rrna

16S rRNA amplicon sequencing analysis workflow using QIIME2

Version 2.1.1   Published 1 month ago

399 nf-core/rnaseq

rna rna-seq

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

Version 3.4   Published 2 months ago

33 nf-core/bacass

assembly bacterial-genomes denovo denovo-assembly genome-assembly hybrid-assembly nanopore nanopore-sequencing

Simple bacterial assembly and annotation pipeline

Version 2.0.0   Published 3 months ago

51 nf-core/viralrecon

amplicon artic assembly covid-19 covid19 illumina long-read-sequencing metagenomics nanopore ont oxford-nanopore sars-cov-2 variant-calling viral virus

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

Version 2.2   Published 4 months ago

16 nf-core/bcellmagic

b-cell immcantation immunorepertoire repseq

B and T cell repertoire sequencing analysis pipeline using the Immcantation framework

Version 2.0.0   Published 5 months ago

25 nf-core/bactmap

bacteria bacterial bacterial-genome-analysis genomics mapping phylogeny tree

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

Version 1.0.0   Published 6 months ago

31 nf-core/smrnaseq

small-rna smrna-seq

A small-RNA sequencing analysis pipeline

Version 1.1.0   Published 6 months ago

129 nf-core/sarek

annotation cancer gatk4 genomics germline pre-processing somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing

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

Version 2.7.1   Published 6 months ago

32 nf-core/hic

chromosome-conformation-capture hi-c

Analysis of Chromosome Conformation Capture data (Hi-C)

Version 1.3.0   Published 7 months ago

7 nf-core/metaboigniter

identification mass-spectrometry metabolomics ms1 ms2 quantification

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

Version 1.0.1   Published 7 months ago

73 nf-core/methylseq

bisulfite-sequencing dna-methylation methyl-seq

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

Version 1.6.1   Published 7 months ago

8 nf-core/diaproteomics

data-independent-proteomics dia-proteomics openms proteomics

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Version 1.2.4   Published 7 months ago

9 nf-core/clipseq

clip clip-seq peak-calling rna-rbp-interactions

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

Version 1.0.0   Published 7 months ago

3 nf-core/pgdb

cosmic gnomad protein-databases proteogenomics proteomics pypgatk

The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.

Version 1.0.0   Published 7 months ago

93 nf-core/chipseq

chip chip-seq chromatin-immunoprecipitation macs2 peak-calling

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

Version 1.2.2   Published 8 months ago

40 nf-core/scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

Version 1.1.0   Published 8 months ago

4 nf-core/dualrnaseq

dualrna-seq host-pathogen quantification readmapping rna-seq

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

Version 1.0.0   Published 10 months ago

7 nf-core/cageseq

cage cage-seq cageseq-data gene-expression rna

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

Version 1.0.2   Published 11 months ago

13 nf-core/epitopeprediction

epitope epitope-prediction mhc-binding-prediction

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

Version 1.1.0   Published 1 year ago

22 nf-core/proteomicslfq

label-free-quantification openms proteomics

Proteomics label-free quantification (LFQ) analysis pipeline

Version 1.0.0   Published 1 year ago

25 nf-core/hlatyping

dna hla hla-typing immunology optitype personalized-medicine rna

Precision HLA typing from next-generation sequencing data

Version 1.2.0   Published 1 year ago

92 nf-core/atacseq

atac-seq chromatin-accessibiity

ATAC-seq peak-calling, QC and differential analysis pipeline

Version 1.2.1   Published 1 year ago

62 nf-core/rnafusion

fusion fusion-genes gene-fusion rna rna-seq

RNA-seq analysis pipeline for detection gene-fusions

Version 1.2.0   Published 1 year ago

12 nf-core/imcyto

cytometry image-analysis image-processing image-segmentation

Image Mass Cytometry analysis pipeline

Version 1.0.0   Published 2 years ago

4 nf-core/slamseq

differential-expression quantseq slamseq transcriptomics

SLAMSeq processing and analysis pipeline

Version 1.0.0   Published 2 years ago

5 nf-core/coproid

adna ancient-dna coprolite microbiome

Coprolite host Identification pipeline

Version 1.1   Published 2 years ago

3 nf-core/nascent

gro-seq nascent pro-seq rna transcription

Nascent Transcription Processing Pipeline

Version 1.0   Published 3 years ago