Flexible taxonomic assignment of ambiguous sequencing reads

Background: To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results: We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six differen...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: José Carlos Clemente, Jesper Jansson, Gabriel Valiente
• Keywords: Ambiguous Reads, Artificial Intelligence, BMCBI 2011, Lowest Common Ancestor, Reference Taxonomy