nextclade

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Here are 9 public repositories matching this topic...

UPHL-BioNGS / Cecret

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Reference-based consensus creation

Updated Aug 7, 2026
Nextflow

UPHL-BioNGS / walkercreek

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A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.

Updated Jun 9, 2026
Nextflow

neherlab / nextclade_data_workflows

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snakemake phylogenetics nextstrain virus-evolution nextclade

Updated Aug 3, 2026
Python

AdrianLimaG / Influenza_Pipeline

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KDHE Influenza A pipeline, built to take MinIon fastq files and produce clade analysis

bioinformatics-pipeline irma minion influenza kansas nextclade

Updated Jan 31, 2023
Perl

cmkobel / pipe19

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This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)

illumina-sequencing pangolin gwf-org nextclade ivar-consensus

Updated May 17, 2021
R

marithetland / susCovONT

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Pipeline to generate consensus.fasta files and identify pangolin lineage and nextstrain clade of Sars-CoV-2 genomes from ONT sequencing

pangolin artic covid-19 sars-cov-2 nextclade

Updated Feb 21, 2023
Python

enterovirus-phylo / Nextclade-dataset-template

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A template for building a custom Enterovirus Nextclade dataset

template nextclade enterovirus

Updated Jul 21, 2026
Python

enterovirus-phylo / nextclade_d68

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Snakemake pipeline for creating a Nextclade dataset for Enterovirus D68

nextclade enterovirus ev-d68

Updated Aug 7, 2026
Python

enterovirus-phylo / nextclade_a16

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nextclade enterovirus cva16

Updated Aug 3, 2026
Python

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