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v1.3.0
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@j3551ca j3551ca released this 28 Jul 18:25
· 78 commits to main since this release
v1.3.0
094ad4d

  • Option to run pipeline on individual samples (default: 1 x for fq, 1 x rev fq) or on the combined result of multiple replicates (ex. 3 x for, 3 x rev)

  • Mutation table functionality - cleaned and formatted output of Freebayes-called, SnpEff-annotated mutations per sample in input directory when --annotate_snps active plus option to combine this output across multiple directories specified by --table_search_string

  • Optional bootstrapping functionality - Freyja bootstrapped estimates of lineage & WHO VOC/VOI

  • Freyja kept at v1.4.2 for validation purposes

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