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nf-core/eager
2.5.3
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adna ancient-dna-analysis ancientdna genome
+3
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A fully reproducible and state-of-the-art ancient DNA analysis pipeline
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nf-core/epigenomesegmentation
0.0.0-09de6dc
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epigenome multi-omics-integration segmentation
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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.
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nf-core/epitopeprediction
3.1.1
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epitope epitope-prediction mhc-binding-prediction
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A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
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nf-core/evexplorer
0.0.0-c5677f2
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extracellular-vesicles ont
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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)
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nf-core/exoseq
0.0.0-600fad3
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exome exome-sequencing genomics variant-calling
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Please consider using/contributing to https://github.com/nf-core/sarek
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nf-core/fastqrepair
1.1.1
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corruption data-cleaning data-recovery fastq
+6
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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
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nf-core/fastquorum
2.0.0
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consensus umi umis unique-molecular-identifier
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Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
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nf-core/fetchngs
1.13.0
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ddbj download ena fastq
+3
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Pipeline to fetch metadata and raw FastQ files from public databases
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nf-core/funcprofiler
1.0.0
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n/a
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Read-based functional profiling of microbiome sequencing data
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nf-core/funcscan
4.0.0
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amp amr antibiotic-resistance antimicrobial-peptides
+11
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(Meta-)genome screening for functional and natural product gene sequences
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nf-core/genephylomodeler
0.0.0-2612665
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evolutionary-models msa natural-selection phylogenetics
+1
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A bioinformatics pipeline that fits evolutionary models and detects natural selection from multiple sequence alignments
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nf-core/genomeannotator
0.0.0-1af305a
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annotation assembly draft-genome gene-annotation
+2
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Pipeline for the identification of (coding) gene structures in draft genomes.
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nf-core/genomeassembler
2.0.0
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genome-assembly
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Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
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nf-core/genomeqc
1.0.1
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genome-assembly-evaluation genomics phylogenetic-trees quality-control
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Compare the quality of multiple genomes, along with their annotations.
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nf-core/genomeskim
0.0.0-ba97621
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chloroplast-genome genome genome-skimming mitochondrial-genomes
+1
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QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
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nf-core/genomicrelatedness
0.0.0-8dec64e
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wgs
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Bioinformatics pipeline for estimating genetic relatedness from low-coverage whole-genome sequencing (sWGS) data
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nf-core/gwas
0.0.0-b8c3ea9
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gwas
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UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
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nf-core/hadge
1.0.0
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cell-hashing deconvolution demultiplexing donor-assignment
+7
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Comprehensive pipeline for donor demultiplexing in single cell
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nf-core/hgtseq
1.1.0
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bwa-mem bwa-mem2 fastqc genomics-visualization
+9
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A pipeline to investigate horizontal gene transfer from NGS data
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nf-core/hic
2.1.0
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chromosome-conformation-capture hi-c
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Analysis of Chromosome Conformation Capture data (Hi-C)
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