PT  - JOURNAL ARTICLE
AU  - Patrick D. Schloss
TI  - Application of database-independent approach to assess the quality of OTU picking methods
AID  - 10.1101/042812
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 042812
4099  - http://biorxiv.org/content/early/2016/03/08/042812.short
4100  - http://biorxiv.org/content/early/2016/03/08/042812.full
AB  - Assigning 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database. I have applied the Matthew’s correlation coefficient to assess the ability of 15 reference-independent and-dependent clustering algorithms to assign sequences to OTUs. This metric quantifies the ability of an algorithm to reflect the relationships between sequences without the use of a reference and can be applied to any dataset or method. The most consistently robust method was the average neighbor algorithm; however, for some datasets other algorithms matched its performance.