title: Metabarcoding of marine nematodes - evaluation of similarity scores used in alignment-based taxonomy assignment approach.
abstract: BACKGROUND
  The diversity of organisms is being commonly accessed using metabarcoding of environmental samples. Reliable identification of barcodes is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task, including alignment-based approach that uses Basic Local Alignment Search Tool (BLAST) algorithm. This publication evaluates the variability of 5' end of 18S rRNA barcoding region as expressed by similarity scores (alignment score and identity score) produced by BLAST, and its impact on barcode identification to family-level taxonomic categories.
  
  
  CONCLUSIONS
  In alignment-based taxonomy assignment approach, reliable identification of anonymous OTUs to supraspecific taxa depends on the correct application of similarity thresholds. Since various taxa show different level of genetic variation, practical application of alignment-based approach requires the determination and use of taxon-specific similarity thresholds.
authors.affiliation: Swedish Museum of Natural History, Stockholm, Sweden.
authors.forename: Oleksandr
authors.initials: O
authors.lastname: Holovachov
keywords:  Nematoda ; 18S rRNA; BLAST; OTU; alignment-based approach.; metabarcoding; taxonomy assignment