We present KrakenLinked, a metagenomic read classifier for Linked-Reads. We have formulated two algorithms for read classification of metagenomic samples using linked reads: tree pruning and taxa promotion. Tree pruning improves specificity while taxa promotion improves sensitivity. Used together the algorithms improve the taxonomic classification of linked-reads compared to short reads, particularly reducing false identification of taxa. We have implemented these algorithms as functions in KrakenUniq which we make available as KrakenLinked.

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