A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle
المؤلفون المشاركون
Kibegwa, Felix M.
Bett, Rawlynce C.
Gachuiri, Charles K.
Stomeo, Francesca
Mujibi, Fidalis D.
المصدر
العدد
المجلد 2020، العدد 2020 (31 ديسمبر/كانون الأول 2020)، ص ص. 1-12، 12ص.
الناشر
Hindawi Publishing Corporation
تاريخ النشر
2020-04-23
دولة النشر
مصر
عدد الصفحات
12
التخصصات الرئيسية
الملخص EN
Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines.
These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis.
In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters.
Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes.
Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively.
933 species were detected by the two algorithms.
Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely.
For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species.
54 genera and 72 species were commonly detected by the two methods.
Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample.
This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected.
However, Kraken 2 generated a more accurate taxonomic identification given the higher number of “Unclassified” reads in MG-RAST.
The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data.
The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.
نمط استشهاد جمعية علماء النفس الأمريكية (APA)
Kibegwa, Felix M.& Bett, Rawlynce C.& Gachuiri, Charles K.& Stomeo, Francesca& Mujibi, Fidalis D.. 2020. A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle. BioMed Research International،Vol. 2020, no. 2020, pp.1-12.
https://search.emarefa.net/detail/BIM-1132450
نمط استشهاد الجمعية الأمريكية للغات الحديثة (MLA)
Kibegwa, Felix M.…[et al.]. A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle. BioMed Research International No. 2020 (2020), pp.1-12.
https://search.emarefa.net/detail/BIM-1132450
نمط استشهاد الجمعية الطبية الأمريكية (AMA)
Kibegwa, Felix M.& Bett, Rawlynce C.& Gachuiri, Charles K.& Stomeo, Francesca& Mujibi, Fidalis D.. A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle. BioMed Research International. 2020. Vol. 2020, no. 2020, pp.1-12.
https://search.emarefa.net/detail/BIM-1132450
نوع البيانات
مقالات
لغة النص
الإنجليزية
الملاحظات
Includes bibliographical references
رقم السجل
BIM-1132450
قاعدة معامل التأثير والاستشهادات المرجعية العربي "ارسيف Arcif"
أضخم قاعدة بيانات عربية للاستشهادات المرجعية للمجلات العلمية المحكمة الصادرة في العالم العربي
تقوم هذه الخدمة بالتحقق من التشابه أو الانتحال في الأبحاث والمقالات العلمية والأطروحات الجامعية والكتب والأبحاث باللغة العربية، وتحديد درجة التشابه أو أصالة الأعمال البحثية وحماية ملكيتها الفكرية. تعرف اكثر