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Oct 12, 2025 - Python
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nextclade
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This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)
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May 17, 2021 - R
Pipeline to generate consensus.fasta files and identify pangolin lineage and nextstrain clade of Sars-CoV-2 genomes from ONT sequencing
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Feb 21, 2023 - Python
Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis for G and F versus NC_038235.1 and NC_001781.1. Includes CI and environment files for easy setup.
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Sep 30, 2025 - Python
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