A community effort to collect a curated set of analysis pipelines built using Nextflow
Pipeline release! nf-core/airrflow v5.0.0 - Tarantallegra!
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Please see the changelog: https://github.com/nf-core/airrflow/releases/tag/5.0.0
#airr #bcell #immcantation #immunorepertoire #repseq #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/mag v5.4.0 - mag 5.4.0 - Yellow Frog!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.4.0
#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/hlatyping v2.2.0 - 2.2.0 - Holocron!
Precision HLA typing from next-generation sequencing data
Please see the changelog: https://github.com/nf-core/hlatyping/releases/tag/2.2.0
#dna #hla #hlatyping #immunology #optitype #personalizedmedicine #rna #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/nanostring v1.3.3 - v1.3.3 - 2026-01-30 - Micrometer patch 3!
An analysis pipeline for Nanostring nCounter expression data.
Please see the changelog: https://github.com/nf-core/nanostring/releases/tag/1.3.3
#nanostring #nanostringnorm #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/demo v1.1.0 - nf-core/demo 1.1.0 - Grammar Police!
nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
Please see the changelog: https://github.com/nf-core/demo/releases/tag/1.1.0
#demo #minimalexample #training #tutorial #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/pairgenomealign v2.2.2 - nf-core/pairgenomealign v2.2.2 – Juicy!
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/2.2.2
#comparativegenomics #dotplot #genomics #last #pairwisealignment #synteny #wholegenomealignment #nfcore #openscience #nextflow #bioinformatics
🧑💻 Need help with #nfcore #nextflow #bioinformatics pipelines, running or developing?
Please join the 🌍🌎 Eur/M.E./Afr/Americas weekly helpdesk.
Please join our nf-core maintainer @vagkaratzas, this Thursday at 14:30 CET | 08:30 ET on https://play.workadventu.re/@/nf-core/nf-core/office
Pipeline release! nf-core/viralmetagenome v1.1.0 - v1.1.0 - Virid Hen!
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.0
#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/ampliseq v2.16.1 - Ampliseq release 2.16.1 2026-01-23!
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.16.1
#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #metataxonomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/pixelator v2.3.1 - nf-core/pixelator 2.3.1!
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/2.3.1
#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/ampliseq v2.16.0 - Ampliseq Version 2.16.0!
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.16.0
#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #metataxonomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/nanostring v1.3.2 - v1.3.2 - 2026-01-15 - Micrometer patch 2!
An analysis pipeline for Nanostring nCounter expression data.
Please see the changelog: https://github.com/nf-core/nanostring/releases/tag/1.3.2
#nanostring #nanostringnorm #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/mhcquant v3.1.0 - 3.1.0 - BlüBa!
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Please see the changelog: https://github.com/nf-core/mhcquant/releases/tag/3.1.0
#dda #immunopeptidomics #massspectrometry #mhc #openms #peptides #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/smrnaseq v2.4.1 - v2.4.1 - 2026-01-07 - Navy Iron Boxer Patch!
A small-RNA sequencing analysis pipeline
Please see the changelog: https://github.com/nf-core/smrnaseq/releases/tag/2.4.1
#smallrna #smrnaseq #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/proteinfamilies v2.2.0 - Mercury Spider!
Generation and updating of protein families
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.2.0
#metagenomics #proteinfamilies #proteomics #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/pixelator v2.3.0 - nf-core/pixelator 2.3.0!
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/2.3.0
#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/methylseq v4.2.0 - Tapus Maximus!
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth MethylDackel
Please see the changelog: https://github.com/nf-core/methylseq/releases/tag/4.2.0
#bisulfitesequencing #dnamethylation #emseq #epigenome #epigenomics #methylseq #pbat #rrbs #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/rnaseq v3.22.2 - nf-core/rnaseq v3.22.2 - Perfect Palladium Penguin!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.22.2
Pipeline release! nf-core/sarek v3.7.1 - 3.7.1 - Buollámtjåhkka!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.1
#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/oncoanalyser v2.3.0 - 2.3.0 - Spotted Nightjar!
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Please see the changelog: https://github.com/nf-core/oncoanalyser/releases/tag/2.3.0
#cancer #clinical #dna #exome #ngs #panel #rna #targeted #wgs #wigits #wts #nfcore #openscience #nextflow #bioinformatics