nf-core

nf-core/viralmetagenome

A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

40 stars 14 forks 40 watchers Nextflow MIT License
epidemiology fastq nextflow nf-core ngs pipeline viral-metagenomics virology virus-genomes workflow
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4 Open Issues Need Help Last updated: Aug 28, 2026

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Multiqc report includes contig taxonomic classifications 26 days ago
enhancement help wanted priority
nf-core/viralmetagenome
40

A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

Nextflow
#epidemiology#fastq#nextflow#nf-core#ngs#pipeline#viral-metagenomics#virology#virus-genomes#workflow
Optionally use host-filtered reads in downstream mapping steps 26 days ago
enhancement help wanted priority
nf-core/viralmetagenome
40

A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

Nextflow
#epidemiology#fastq#nextflow#nf-core#ngs#pipeline#viral-metagenomics#virology#virus-genomes#workflow
Make custom annotation database using ncbi virus 26 days ago
documentation good first issue priority website
nf-core/viralmetagenome
40

A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

Nextflow
#epidemiology#fastq#nextflow#nf-core#ngs#pipeline#viral-metagenomics#virology#virus-genomes#workflow
Add support for metabuli 26 days ago
enhancement help wanted
nf-core/viralmetagenome
40

A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

Nextflow
#epidemiology#fastq#nextflow#nf-core#ngs#pipeline#viral-metagenomics#virology#virus-genomes#workflow