Work

Novel Algorithms for the Taxonomic Classification of Metagenomic Linked-Reads

Year: 2019

Type: preprint

Abstract: 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 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.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/549667

Authors: David C. Danko, Dmitry Meleshko, Daniela Bezdan, Christopher Mason, Iman Hajirasouliha

Institutions: Cornell University, Weill Cornell Medicine

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Science Foundation, National Institutes of Health, Weill Cornell Medical College

Awards: EAGER: Novel Computational Models and Algorithms for Mapping Link-Read Sequencing Data, G9000147831