scholarly journals Erratum for Salipante et al., Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

2016 ◽  
Vol 82 (14) ◽  
pp. 4453-4453 ◽  
Author(s):  
Stephen J. Salipante ◽  
Toana Kawashima ◽  
Christopher Rosenthal ◽  
Daniel R. Hoogestraat ◽  
Lisa A. Cummings ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
16S Rrna ◽  
Performance Comparison ◽  
Ion Torrent ◽  
Next Generation ◽  
Community Profiling ◽  
Sequencing Platforms ◽  
Generation Sequencing

scholarly journals Bacterial abundance and community composition in green, brown and red water from intensive catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia

2021 ◽  
Vol 22 (9) ◽  
Author(s):  
Karunia Adetera Nungki Wijayanti ◽  
Indah Istiqomah ◽  
Murwantoko Murwantoko
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Water Samples ◽  
Bacterial Abundance ◽  
Rrna Gene ◽  
Next Generation ◽  
Aquaculture System ◽  
Generation Sequencing

Abstract. Wijayanti KAN, Istiqomah I, Murwantoko. 2021. Bacterial abundance and community composition in green, brown and red water from intensive Catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia. Biodiversitas 22: 3677-3684. Catfish (Clarias sp.) is an important aquaculture commodity in Indonesia and cultured in an intensive system. Microorganisms play an important role in maintaining water quality of aquaculture system. The objective of this study was to determine the bacterial abundance and community composition of green, brown and red water collected from intensive catfish culture ponds in Yogyakarta using next-generation sequencing method. The water samples were collected from intensive catfish culture ponds with different colors, namely green, brown and red ponds located in Yogyakarta. The DNA from water samples was extracted using DNA extraction kit and used as template for 16S rRNA amplification. The V3-V4 hypervariable regions of the 16S rRNA gene were amplified apply for next-generation sequencing technology. This study could explore effectively the bacterial community in water samples. The bacterial communities in this catfish culture water showed higher bacterial richness compared to the other aquaculture system. The diversity of the green, brown and red catfish culture water ponds was similar with the number OTUs of the green, brown and red water samples, which were 1269; 1387 and 1323 OTUs respectively. The 694 OTUs (34.42%) were common core microbiomes in all catfish culture ponds, the 212 OTUs (10.51%) are present on green and brown water ponds, the 182 OTUs (9.02%) were on green and red water ponds, and the 183 OTUs (9.07%) were present on green and brown water ponds. However, the composition of the bacterial community was different. The most dominant phylum in green and brown water ponds was Proteobacteria with relative abundance in green water and brown water 71.6% and 47.0% respectively, whereas, the most dominant phylum in red water was Firmicutes (29.5%). The dominance of Firmicutes phylum in red water ponds may be caused by application of probiotic bacteria, the high organic content, and low oxygen concentration.

scholarly journals Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Stéphanie Raymond ◽  
Florence Nicot ◽  
Nicolas Jeanne ◽  
Olivier Delfour ◽  
Romain Carcenac ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Performance Comparison ◽  
Next Generation ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

2014 ◽  
Vol 80 (24) ◽  
pp. 7583-7591 ◽  
Author(s):  
Stephen J. Salipante ◽  
Toana Kawashima ◽  
Christopher Rosenthal ◽  
Daniel R. Hoogestraat ◽  
Lisa A. Cummings ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Error Rates ◽  
Personal Genome ◽  
Rrna Gene ◽  
Ion Torrent ◽  
Community Profiling ◽  
Sequencing Platforms ◽  
Ion Torrent Platform

ABSTRACTHigh-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common “benchtop” sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-organism mock bacterial community and a collection of primary human specimens. We observed comparatively higher error rates with the Ion Torrent platform and report a pattern of premature sequence truncation specific to semiconductor sequencing. Read truncation was dependent on both the directionality of sequencing and the target species, resulting in organism-specific biases in community profiles. We found that these sequencing artifacts could be minimized by using bidirectional amplicon sequencing and an optimized flow order on the Ion Torrent platform. Results of bacterial community profiling performed on the mock community and a collection of 18 human-derived microbiological specimens were generally in good agreement for both platforms; however, in some cases, results differed significantly. Disparities could be attributed to the failure to generate full-length reads for particular organisms on the Ion Torrent platform, organism-dependent differences in sequence error rates affecting classification of certain species, or some combination of these factors. This study demonstrates the potential for differential bias in bacterial community profiles resulting from the choice of sequencing platform alone.

scholarly journals A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 341 ◽  
Author(s):  
Michael Quail ◽  
Miriam E Smith ◽  
Paul Coupland ◽  
Thomas D Otto ◽  
Simon R Harris ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Ion Torrent ◽  
Next Generation ◽  
Pacific Biosciences ◽  
Sequencing Platforms ◽  
Generation Sequencing

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

scholarly journals The Accuracy, Feasibility and Challenges of Sequencing Short Tandem Repeats Using Next-Generation Sequencing Platforms

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e113862 ◽  
Author(s):  
Monika Zavodna ◽  
Andrew Bagshaw ◽  
Rudiger Brauning ◽  
Neil J. Gemmell
Keyword(s):  
Next Generation Sequencing ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Next Generation ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Short Tandem
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