Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.
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TLDR
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines and can reliably identify barcodes and assign the reads to the original samples.About:
This article is published in Genomics.The article was published on 2011-08-01 and is currently open access. It has received 480 citations till now. The article focuses on the topics: Adapter (computing).read more
Citations
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Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses.
Xing Guo,Xin-Xin He,Hong Chen,Zhicheng Wang,Hui-Fang Li,Wang Jiangxian,Ming-Shan Wang,Runshen Jiang +7 more
TL;DR: The results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought.
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Characterization of basal and lipopolysaccharide-induced microRNA expression in equine peripheral blood mononuclear cells using Next-Generation Sequencing.
Nicholas J. Parkinson,Virginia Buechner-Maxwell,Sharon G. Witonsky,R. Scott Pleasant,Stephen R. Werre,S. Ansar Ahmed +5 more
TL;DR: The central hypothesis of this study was that lipopolysaccharide induces differential microRNA expression in equine peripheral blood mononuclear cells in a manner comparable to humans, and this will facilitate inter-species comparative study of the role of microRNAs in the inflammatory cascade during endotoxemia and sepsis.
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The microbiota as a candidate biomarker for SPA pools and SPA thermal spring stability after seismic events.
TL;DR: The observed results confirm the impact of the earthquake on the microbiota structure of the underground thermal spring water, suggesting further perspectives for monitoring water stability and safety issues by a metagenomic approach.
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Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium.
Shijie Bai,Peijun Zhang,Changhao Zhang,Jiang Du,Xinyi Du,Chengwei Zhu,Jun Liu,Peiyu Xie,Songhai Li +8 more
TL;DR: In this article, the authors exploited a natural experiment provided by an aquarium with belugas (Delphinapterus leucas) affiliated with family Monodontidae, Pacific white-sided dolphins (Lagenorhynchus obliquidens) and common bottlenose dolphin (Tursiops truncatus), affiliated with the family Delphinidae, and Cape fur seals (Arctocephalus pusillus pusillus) associated with family Otariidae, to reveal significant differences in microbial community composition of whales, dolphins, and fur seals and
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The Beta-Diversity of Siganus fuscescens-Associated Microbial Communities From Different Habitats Increases With Body Weight.
Yongjie Wu,Fanshu Xiao,Cheng Wang,Longfei Shu,Xiafei Zheng,Kui Xu,Xiaoli Yu,Keke Zhang,Hongtian Luo,Yufeng Yang,Zhili He,Zhili He,Qingyun Yan +12 more
TL;DR: This study systematically studied the microbial communities of 108 wild S. fuscescens in four body habitats and surrounding water to enhance mechanistic understanding of fish-associated microbial communities in different habitats, and has important implications for analyzing host-associated metacommunities.
References
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A fast bit-vector algorithm for approximate string matching based on dynamic programming
TL;DR: An algorithm of comparable simplicity that requires only O(kn/w) time by virtue of computing a bit representation of the relocatable dynamic programming matrix for the approximate string matching problem, and is found to be more efficient than the previous results for many choices of k and small.