TY - DATA T1 - Supporting data for "Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments" AU - Aleksandra, Tarkowska AU - Alex, Mitchell L AU - Alexandre, Almeida AU - Robert, Finn D DO - 10.5524/100448 UR - http://gigadb.org/dataset/100448 AB - Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. QIIME and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene.
We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently below 2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost two and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher recall than using Greengenes, while assignment results of different 16S rRNA variable sub-regions varied up to 40% between samples analysed with the same pipeline.
Our results support the use of either QIIME 2 or MAPseq for optimal 16S rRNA gene profiling, and we suggest that the choice between the two should be based on the level of recall, precision and/or computational performance required. KW - Software KW - Metagenomic KW - 16s rrna gene KW - human gastrointestinal tract KW - ocean KW - microbiome KW - soil KW - taxonomy PY - 2018 PB - GigaScience Database LA - en ER -