Comparison of Methods for Picking the Operational Taxonomic Units From Amplicon Sequences
نویسندگان
چکیده
منابع مشابه
From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at diffe...
متن کاملOptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassign...
متن کاملA heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units
A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ...
متن کاملDe novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its abil...
متن کاملApplication of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods
Assignment of 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 Matthews correlation coefficient to assess the ability of 15 reference-independent and -de...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Frontiers in Microbiology
سال: 2021
ISSN: 1664-302X
DOI: 10.3389/fmicb.2021.644012