Resumen:
Sequencing the 16S gene rRNA has become a popular method when identifying bacterial communities. However,
recent studies address differences in the characterization based on sample preparation, sequencing platforms,
and data analysis. In this work, we tested some of the available user-friendly protocols for data analysis with the
reads obtained from the sequencing machines Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM).
We sought for the advantages and disadvantages of both platforms in terms of accuracy, detected species, and
abundance, analyzing a staggered mock community. Four different pipelines were applied: QIIME 1.9.1 with
default parameters, QIIME 1.9.1 with modified parameters and chimera removal, VSEARCH 2.3.4, and QIIME 2
v.2018.2. To address the limitations of species level detection we used species-classifier SPINGO. The optimal
pipeline for PGM platform, was the use of QIIME 1.9.1 with default parameters (QIIME1), except when a study
requires the detection of Bacteroides or other Bacteroidaceae members, in which QIIME1MOD (with chimera
removal) seems to be a good alternative. For Illumina Miseq, VSEARCH strategy can be a good option. Our
results also confirm...