Identify unique combinations of taxids before running NCBI topology#4
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maxibor merged 3 commits intomaxibor:masterfrom Aug 20, 2021
Merged
Identify unique combinations of taxids before running NCBI topology#4maxibor merged 3 commits intomaxibor:masterfrom
maxibor merged 3 commits intomaxibor:masterfrom
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Reduces the run time of sam2lca by identifying all unique combinations of taxids that were observed across all reads and by running the expensive NCBI topology function of ete3 on these. For samples that have a lot of aligned reads but only a few combinations of taxids, this will decrease the number of lookups strongly.
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Reduces the run time of sam2lca by identifying all unique combinations of taxids that were observed across all reads and by running the expensive NCBI topology function of ete3 on these. For samples that have a lot of aligned reads but only a few combinations of taxids, this will decrease the number of lookups strongly.