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pangolin

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End to end Snakemake workflow for iSeq amplicon data. FastQC, Trimmomatic, BWA, SAMtools and bcftools consensus at depth 10, Pangolin lineage assignment, MAFFT alignment, IQ-TREE with ultrafast bootstraps and optional ModelFinder, optional Augur plus TreeTime for time-resolved trees, and utilities to fetch context genomes from GenBank.

  • Updated Jun 1, 2026
  • Python

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