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nf-core/bacass
2.6.1
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assembly bacterial-genomes denovo denovo-assembly
+4
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Simple bacterial assembly and annotation pipeline
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nf-core/bacmodel
0.0.0-c6948d4
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bacteria genome-scale-models metabolic-models metaomics
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Systems-based bacterial functional modeling pipeline
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nf-core/bactmap
1.0.0
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bacteria bacterial bacterial-genome-analysis genomics
+3
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A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
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nf-core/denovohybrid
0.0.0-9299621
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assembly denovo denovo-assembly genome-assembly
+4
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UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads
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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/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/mag
5.5.0
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annotation assembly binning long-read-sequencing
+4
|
Assembly and binning of metagenomes
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nf-core/methylseq
4.2.0
|
bisulfite-sequencing dna-methylation em-seq epigenome
+6
|
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
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nf-core/neutronstar
1.0.0
|
10x-genomics 10xgenomics denovo-assembly genome-assembly
+2
|
De novo assembly pipeline for 10X linked-reads using Supernova
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nf-core/pairgenomealign
3.0.4
|
comparative-genomics dot-plot genomics last
+3
|
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
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nf-core/pangenome
1.1.3
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pangenome
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Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
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nf-core/references
0.1.0
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genome references reproducibility
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nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
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nf-core/sammyseq
0.0.0-023aff4
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3d-genome chromatin dna epigenetics
+6
|
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
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nf-core/sarek
3.10.0
|
annotation cancer gatk4 genomics
+7
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Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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nf-core/vipr
0.0.0-6eef3b3
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genome-assembly metagenomics variant-calling viral
+5
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Assembly and intrahost / low-frequency variant calling for viral samples
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nf-core/viralmetagenome
1.2.0
|
epidemiology fastq ngs viral-metagenomics
+2
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A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
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