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Nextflow Pipelines

Nextflow pipelines hosted in Git repositories. Each published release records the Git revision it runs and the launch configuration it ships with.

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12 pipeline(s) matching "metagenomics".

Pipeline Keywords Description
nf-core/ampliseq
3.0.0
 16s 18s amplicon-sequencing edna +12 Amplicon sequencing analysis workflow using DADA2 and QIIME2
nf-core/createtaxdb
3.1.0
 database database-builder metagenomic-profiling metagenomics +2 Parallelised and automated construction of metagenomic classifier databases of different tools
nf-core/detaxizer
1.3.0
 de-identification decontamination edna fastq +10 A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
nf-core/eager
2.5.3
 adna ancient-dna-analysis ancientdna genome +3 A fully reproducible and state-of-the-art ancient DNA analysis pipeline
nf-core/funcscan
4.0.0
 amp amr antibiotic-resistance antimicrobial-peptides +11 (Meta-)genome screening for functional and natural product gene sequences
nf-core/mag
5.5.0
 annotation assembly binning long-read-sequencing +4 Assembly and binning of metagenomes
nf-core/metatdenovo
2.0.0
 eukaryotes metagenomics metatranscriptomics prokaryotes +1 Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
nf-core/proteinfamilies
2.6.0
 metagenomics protein-families Generation and updating of protein families
nf-core/taxprofiler
2.0.1
 classification illumina long-reads metagenomics +7 Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core/vipr
0.0.0-6eef3b3
 genome-assembly metagenomics variant-calling viral +5 Assembly and intrahost / low-frequency variant calling for viral samples
nf-core/viralmetagenome
1.2.0
 epidemiology fastq ngs viral-metagenomics +2 A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
nf-core/viralrecon
3.0.0
 amplicon artic assembly covid-19 +11 Assembly and intrahost/low-frequency variant calling for viral samples
Nextflow Registry v0.28.0_c73a300 - 12 Oct 2026 09:32:30 (UTC)