kallisto is a program for quantifying abundances of transcripts from RNA-Seq data. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Bracken (Bayesian Reestimation of Abundance with KrakEN): re-estimates species/genus-level
Name, KrakenReport
Name, BrackenAbundance [File], BrackenReport [File], KrakenReport [File], Live Report [Link]
NfCoreAmpliseqApp
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Name
Name, Result [File], MultiQC [Link]
NfCoreCreatetaxdbApp
Parallelised and automated construction of metagenomic classifier databases of different tools
Name
Name, Result [File], MultiQC [Link]
NfCoreDetaxizerApp
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
Name
Name, Result [File], MultiQC [Link]
NfCoreEagerApp
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreFuncscanApp
(Meta-)genome screening for functional and natural product gene sequences
Name
Name, Result [File], MultiQC [Link]
NfCoreMagApp
Assembly and binning of metagenomes
Name
Name, Result [File], MultiQC [Link]
NfCoreMetatdenovoApp
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
Name
Name, Result [File], MultiQC [Link]
NfCoreProteinfamiliesApp
Generation and updating of protein families
Name
Name, Result [File], MultiQC [Link]
NfCoreTaxprofilerApp
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Name
Name, Result [File], MultiQC [Link]
NfCoreViralreconApp
Assembly and intrahost/low-frequency variant calling for viral samples
Name
Name, Result [File], MultiQC [Link]
NestLinkApp
NestLink - an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles - https://bioconductor.org/packages/release/data/experiment/html/NestLink.html
Name, Read1, FlashLog
Name, NestLink Result [File]
ConvERDSApp
This converts the result DataSet of EAGLERCApp to an input DataSet of DNAHaplotypeCallerGVCFApp.
Name, Species, dummy
Name, BAM, refBuild, Species, Dummy [File]
EAGLERCApp
EAGLE: Explicit Alternative Genome Likelihood Evaluator
This pipeline performs the peptide identification of MS2 spectra from a proteomics experiment. For this, different search algorithm and rescoring approaches can be selected.
Name
Name, Result [File], MultiQC [Link]
EnaApp
Download public data from ENA
Name, projectID
Name, projectID, ENA Result [File]
BuscoApp
BUSCO: from QC to gene prediction and phylogenomics
NanoPlot: Plotting tool for long read sequencing data and alignments
Name, Read1
Name, NanoPlot Result [File], Report [Link]
QuastApp
QUAST (Quality Assessment Tool for Genome Assemblies)
Name, Draft
Name, QuastReport [Link], QuastOut [File], Species
RnaBamStatsApp
Quality control after the alignment of RNAseq reads
Name, BAM, BAI, refBuild, Species
Name, Report [File], Html [Link], Species, refBuild, refFeatureFile
RnaBiasApp
Name, Read1, Species, Order Id, PlateName
Name, Report [File,Link]
PreqcApp
Preqc - Illumina read pre-assembly quality control and data exploration module within sga
Name, Read1, Read2
Name, PreqcReport [File,Link], PreqcOut [File]
ONTwfAAVqcApp
QC of recombinant adeno-associated viral vector (rAAV) preparations.
Name, Read1
Name, OutDir [File], OutReport [Link]
NfCoreGenomeqcApp
Compare the quality of multiple genomes, along with their annotations.
Name
Name, Result [File], MultiQC [Link]
NfCoreScdownstreamApp
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Name
Name, Result [File], MultiQC [Link]
NfCoreSeqinspectorApp
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
Name
Name, Result [File], MultiQC [Link]
NfCoreTumourevoApp
Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
Name
Name, Result [File], MultiQC [Link]
BDRhapsodySAApp
This wrapper runs a CWL workflow for the analysis of BD Single-Cell Multiomics.
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. It is often also referred to by its French name, Le plieur de cellules. ToolLink: https://github.com/broadinstitute/CellBender
Merging more than two DataSets generaged from same library for CellRangerApp
Name, Species, RawDataDir
Name, Species
ONTwfScApp
A research pipeline designed to identify the cell barcode and UMI sequences present in nanopore sequencing reads generated from single-cell gene expression libraries
Name, VCF [File], VCFINDEX [File], Other [File], Species, refBuild
PbsvApp
pbsv - PacBio structural variant (SV) calling and analysis tools
Name, BAM, BAI, refBuild
Name, refBuild, OutDir [File], OutReport [Link]
DellyApp
delly uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
Name, BAM, BAI, refBuild
Name, refBuild, OutDir [File], OutReport [Link]
GatkJoinGenoTypesRNASeqApp
genotype,merge and annotate gvcf-Files
Name, GVCF, GVCFINDEX, Species, refBuild
Name, Report [File], Html [Link], Species, refBuild
NfCoreDiseasemodulediscoveryApp
A pipeline for network-based disease module identification.
Name
Name, Result [File], MultiQC [Link]
NfCoreCoproidApp
Coprolite host Identification pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreAirrflowApp
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Name
Name, Result [File], MultiQC [Link]
NfCoreNanoseqApp
Nanopore demultiplexing, QC and alignment pipeline
Name
Name, Result [File], MultiQC [Link]
NfCorePacvarApp
Longread PacBio sequencing processing for WGS and PureTarget
Name
Name, Result [File], MultiQC [Link]
NfCoreProteinfoldApp
Protein 3D structure prediction pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreCircdnaApp
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.
Name
Name, Result [File], MultiQC [Link]
NfCoreGenomeannotatorApp
Pipeline for the identification of (coding) gene structures in draft genomes.
Name
Name, Result [File], MultiQC [Link]
NfCoreProteinannotatorApp
Generation of sequence-level annotations for amino acid sequences
Name
Name, Result [File], MultiQC [Link]
NfCoreSarekApp
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Name
Name, Result [File], MultiQC [Link]
NfCoreDeepmodeloptimApp
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
Name
Name, Result [File], MultiQC [Link]
NfCoreBacassApp
Simple bacterial assembly and annotation pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreHicarApp
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
Name
Name, Result [File], MultiQC [Link]
NfCoreBactmapApp
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Name
Name, Result [File], MultiQC [Link]
NfCoreBamtofastqApp
Converts bam or cram files to fastq format and does quality control.
Name
Name, Result [File], MultiQC [Link]
NfCoreDemultiplexApp
Demultiplexing pipeline for sequencing data
Name
Name, Result [File], MultiQC [Link]
NfCoreVariantbenchmarkingApp
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Name
Name, Result [File], MultiQC [Link]
NfCorePathogensurveillanceApp
Surveillance of pathogens using population genomics and sequencing
Name
Name, Result [File], MultiQC [Link]
NfCoreMethylseqApp
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
Name
Name, Result [File], MultiQC [Link]
NfCoreRarevariantburdenApp
Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
Name
Name, Result [File], MultiQC [Link]
NfCoreHgtseqApp
A pipeline to investigate horizontal gene transfer from NGS data
Name
Name, Result [File], MultiQC [Link]
NfCoreCageseqApp
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
Name
Name, Result [File], MultiQC [Link]
NfCoreOncoanalyserApp
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreDrugresponseevalApp
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
Name
Name, Result [File], MultiQC [Link]
NfCoreViralintegrationApp
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
Name
Name, Result [File], MultiQC [Link]
NfCoreGenomeskimApp
QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
Name
Name, Result [File], MultiQC [Link]
NfCoreHicApp
Analysis of Chromosome Conformation Capture data (Hi-C)
Name
Name, Result [File], MultiQC [Link]
NfCoreClipseqApp
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
Name
Name, Result [File], MultiQC [Link]
NfCoreDeepmutscanApp
nf-core/deepmutscan is a reproducible, scalable, and community-curated pipeline for analyzing deep mutational scanning (DMS) data using shotgun DNA sequencing.
Name
Name, Result [File], MultiQC [Link]
NfCorePairgenomealignApp
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
Name
Name, Result [File], MultiQC [Link]
NfCoreFastquorumApp
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
Name
Name, Result [File], MultiQC [Link]
NfCoreFastqrepairApp
A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
Name
Name, Result [File], MultiQC [Link]
NfCoreProteogenomicsdbApp
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
Name
Name, Result [File], MultiQC [Link]
NfCoreCrisprseqApp
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`).
Name
Name, Result [File], MultiQC [Link]
NfCoreCutandrunApp
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
Name
Name, Result [File], MultiQC [Link]
NfCoreImcytoApp
Image Mass Cytometry analysis pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreDartseqApp
Pipeline for m6A detection in RNAseq data
Name
Name, Result [File], MultiQC [Link]
NfCoreDiaproteomicsApp
Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
Name
Name, Result [File], MultiQC [Link]
NfCoreMhcquantApp
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Name
Name, Result [File], MultiQC [Link]
NfCoreFetchngsApp
Pipeline to fetch metadata and raw FastQ files from public databases
Name
Name, Result [File]
NfCoreDemoApp
nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
Name
Name, Result [File], MultiQC [Link]
NfCoreRarediseaseApp
Call and score variants from WGS/WES of rare disease patients.
Name
Name, Result [File], MultiQC [Link]
NfCoreLncpipeApp
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
Name
Name, Result [File], MultiQC [Link]
NfCoreSlamseqApp
SLAMSeq processing and analysis pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreMethylongApp
Extract methylation calls from long reads (ONT/ PacBio)
Name
Name, Result [File], MultiQC [Link]
NfCoreRangelandApp
Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
Name
Name, Result [File], MultiQC [Link]
NfCoreViralmetagenomeApp
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Name
Name, Result [File], MultiQC [Link]
NfCoreEpigenomesegmentationApp
An nf-core pipeline for epigenome segmentation using EpiSegMix/Meth — a hidden Markov model with flexible read count distributions and state duration modeling for histone, open chromatin, and methylation signals.
Name
Name, Result [File], MultiQC [Link]
NfCoreEpitopepredictionApp
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Name
Name, Result [File], MultiQC [Link]
NfCorePhyloplaceApp
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Name
Name, Result [File], MultiQC [Link]
NfCoreGenephylomodelerApp
A bioinformatics pipeline that fits evolutionary models and detects natural selection from multiple sequence alignments
Name
Name, Result [File], MultiQC [Link]
NfCoreStableexpressionApp
This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.
Name
Name, Result [File], MultiQC [Link]
NfCoreEvexplorerApp
nf-core/evexplorer is a pipeline for analyzing RNA data from extracellular vesicles, compatible with technologies such as nextflex, comboSeq, and ONT with further support forthcoming. evexplorer handles QC, expressed region detection, library size normalization and Differential RNA Expression (DRE)
Name
Name, Result [File], MultiQC [Link]
NfCoreRnavarApp
gatk4 RNA variant calling pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreReferencesApp
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
Name
Name, Result [File], MultiQC [Link]
NfCoreGenomeassemblerApp
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
Name
Name, Result [File], MultiQC [Link]
NfCoreNascentApp
Nascent Transcription Processing Pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreGwasApp
UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
Name
Name, Result [File], MultiQC [Link]
NfCoreMetaboigniterApp
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
Name
Name, Result [File], MultiQC [Link]
NfCoreNcrnannotatorApp
nf-core pipeline for genome-level ncRNA annotation using Infernal
Name
Name, Result [File], MultiQC [Link]
NfCoreIsoseqApp
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
Name
Name, Result [File], MultiQC [Link]
NfCoreKmermaidApp
k-mer similarity analysis pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreMnaseseqApp
MNase-seq analysis pipeline using BWA and DANPOS2.
Name
Name, Result [File], MultiQC [Link]
NfCoreTbanalyzerApp
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
Name
Name, Result [File], MultiQC [Link]
NfCoreNanostringApp
An analysis pipeline for Nanostring nCounter expression data.
Name
Name, Result [File], MultiQC [Link]
NfCoreAbotyperApp
A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.
Name
Name, Result [File], MultiQC [Link]
NfCoreAlleleexpressionApp
Alleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
Name
Name, Result [File], MultiQC [Link]
NfCoreCallingcardsApp
A pipeline for processing calling cards data
Name
Name, Result [File], MultiQC [Link]
NfCoreCellpaintingApp
nf-core/cellpainting pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreCreatepanelrefsApp
Generate Panel of Normals, models or other similar references from lots of samples
Name
Name, Result [File], MultiQC [Link]
NfCoreDatasyncApp
nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks
Name
Name, Result [File], MultiQC [Link]
NfCoreDropApp
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Name
Name, Result [File], MultiQC [Link]
NfCoreFuncprofilerApp
Read-based functional profiling of microbiome sequencing data
Name
Name, Result [File], MultiQC [Link]
NfCoreLongrarediseaseApp
Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
Name
Name, Result [File], MultiQC [Link]
NfCoreMagmapApp
Best-practice analysis pipeline for mapping reads to a (large) collections of genomes
Name
Name, Result [File], MultiQC [Link]
NfCoreMeerpipeApp
nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
Name
Name, Result [File], MultiQC [Link]
NfCoreMetapepApp
From metagenomes to epitopes and beyond
Name
Name, Result [File], MultiQC [Link]
NfCoreMethylarrayApp
Process methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
Name
Name, Result [File], MultiQC [Link]
NfCoreMitodetectApp
A-Z analysis of mitochondrial NGS data
Name
Name, Result [File], MultiQC [Link]
NfCoreMultiplesequencealignApp
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
Name
Name, Result [File], MultiQC [Link]
NfCoreOmicsgenetraitassociationApp
A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
Name
Name, Result [File], MultiQC [Link]
NfCorePacsomaticApp
Nextflow pipeline for PacBio HiFi tumor/normal somatic genomics
Name
Name, Result [File], MultiQC [Link]
NfCorePanoramaseqApp
a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays
Name
Name, Result [File], MultiQC [Link]
NfCorePhageannotatorApp
Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
Name
Name, Result [File], MultiQC [Link]
NfCoreRadseqApp
Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).
Name
Name, Result [File], MultiQC [Link]
NfCoreReadsimulatorApp
A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
Name
Name, Result [File], MultiQC [Link]
NfCoreRibomsqcApp
QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis
Name
Name, Result [File], MultiQC [Link]
NfCoreRiboseqApp
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
Name
Name, Result [File], MultiQC [Link]
NfCoreRnadnavarApp
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Name
Name, Result [File], MultiQC [Link]
NfCoreSeqsubmitApp
nf-core pipeline for data submission to ENA
Name
Name, Result [File], MultiQC [Link]
NfCoreSpinningjennyApp
Pipeline for simulating the first industrial revolution using Agent Based Models.
Name
Name, Result [File], MultiQC [Link]
NfCoreVariantcatalogueApp
Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.
Name
Name, Result [File], MultiQC [Link]
NfCoreVariantprioritizationApp
Bioinformatics analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine using Personal Cancer Genome Reporter (PCGR). The pipeline offers germline SNVs/INDELS intepretation and annotation using Cancer Predisposition Sequencing Reporter (CPSR).
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
Name
Name, Result [File], MultiQC [Link]
NfCoreReporthoApp
nf-core pipeline for comparative analysis of ortholog predictions
Name
Name, Result [File], MultiQC [Link]
NfCorePangenomeApp
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
Name
Name, Result [File], MultiQC [Link]
NfCoreTroughgraphApp
A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
Name
Name, Result [File], MultiQC [Link]
NfCoreSopaApp
Nextflow version of Sopa - spatial omics pipeline and analysis
Name
Name, Result [File], MultiQC [Link]
NfCoreSmrnaseqApp
A small-RNA sequencing analysis pipeline
Name
Name, Result [File], MultiQC [Link]
NfCoreGenomicrelatednessApp
Bioinformatics pipeline for estimating genetic relatedness from low-coverage whole-genome sequencing (sWGS) data
