A community effort to collect a curated set of analysis pipelines built using Nextflow
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
Pipeline release! nf-core/rnaseq v3.22.1 - nf-core/rnaseq v3.22.1 - Polished 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/3.22.1
Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!
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/1.0.1
#epidemiology #fastq #ngs #viralmetagenomics #virology #virusgenomes #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.3.0
#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/rnavar v1.2.2 - nf-core/rnavar 1.2.2 - Gray Red Tail!
gatk4 RNA variant calling pipeline
Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.2.2
#gatk4 #rna #rnaseq #variantcalling #worflow #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta!
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/3.7.0
#annotation #cancer #gatk4 #genomics #germline #preprocessing #somatic #targetpanels #variantcalling #wholeexomesequencing #wholegenomesequencing #nfcore #openscience #nextflow #bioinformatics
🧑💻 Need help with #nfcore #nextflow #bioinformatics pipelines, running or developing?
We are merging the 🌍 Eur/M.E./Afr and the 🌎 Americas weekly helpdesk.
Please join our nf-core maintainers, this Thursday at 14:30 CET | 08:30 ET on https://play.workadventu.re/@/nf-core/nf-core/office
Pipeline release! nf-core/variantbenchmarking v1.4.0 - Thin Yasar!
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.4.0
#benchmark #smallvariants #structuralvariants #variantcalling #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/riboseq v1.2.0 - nf-core/riboseq v1.2.0 - Mercury Spider!
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
Please see the changelog: https://github.com/nf-core/riboseq/releases/tag/1.2.0
Pipeline release! nf-core/phaseimpute v1.1.0 - 1.1.0 - Purple Beagle!
A bioinformatics pipeline to phase and impute genetic data
Please see the changelog: https://github.com/nf-core/phaseimpute/releases/tag/1.1.0
#genomics #genotype #imputation #lowpasssequencing #phasing #nfcore #openscience #nextflow #bioinformatics
Pipeline release! nf-core/magmap vv1.0.0 - magmap v1.0.0!
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Please see the changelog: https://github.com/nf-core/magmap/releases/tag/v1.0.0
Pipeline release! nf-core/rnaseq v3.22.0 - nf-core/rnaseq v3.22.0 - 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/3.22.0
🧑💻 Need help with #nfcore #nextflow #bioinformatics pipelines, running or developing?
We are merging the 🌍 Eur/M.E./Afr and the 🌎 Americas weekly helpdesk.
Please join our host @vagkaratzas nf-core maintainer, this Thursday at 14:30 CET | 08:30 ET on https://play.workadventu.re/@/nf-core/nf-core/office
Pipeline release! nf-core/proteinfamilies v2.1.0 - Iron Goat!
Generation and updating of protein families
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.1.0
#metagenomics #proteinfamilies #proteomics #nfcore #openscience #nextflow #bioinformatics
@eric_normandeau Sorry it's a few months later, but we implemented your suggestion I think - if you look our last few release posts, does it work for you?
Pipeline release! nf-core/taxprofiler v1.2.5 - v1.2.5 - Bouncy Basenji Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.5
#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics