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Hyeonwoo Kim,Jiwon Kim,Ji Won Cho,Kwang-Sung Ahn,Dong-Il Park,Sangsoo Kim Korea Genome Organization 2023 Genomics & informatics Vol.21 No.3
Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.
Kim, Jun Young,Cho, Eunae,Kim, Jaehoon,Shin, Hyeonwoo,Roh, Jeongkyun,Thambidurai, Mariyappan,Kang, Chan-Mo,Song, Hyung-Jun,Kim, SeongMin,Kim, Hyeok,Lee, Changhee Optical Society of America 2015 Optics express Vol.23 No.19
<P>We demonstrate that nanocrystalline Al-doped zinc oxide (n-AZO) thin film used as an electron-extraction layer can significantly enhance the performance of inverted polymer solar cells based on the bulk heterojunction of poly[[9-(1-octylnonyl)-9H-carbazole-2,7-diyl]-2,5-thiophenediyl-2,1,3-benzothiadiazole-4,7-diyl-2,5-thiophenediyl] (PCDTBT) and [6,6]-phenyl C<sub>71</sub>-butyric acid methyl ester (PC<sub>70</sub>BM). A synergistic study with both simulation and experiment on n-AZO was carried out to offer a rational guidance for the efficiency improvement. As a result, An n-AZO film with an average grain size of 13 to 22 nm was prepared by a sol-gel spin-coating method, and a minimum resistivity of 2.1 ?? 10<sup>-3</sup> 곽·cm was obtained for an Al-doping concentration of 5.83 at.%. When an n-AZO film with a 5.83 at.% Al concentration was inserted between the ITO electrode and the active layer (PCDTBT:PC<sub>70</sub>BM), the power conversion efficiency increased from 3.7 to 5.6%.</P>