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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Biogeographic patterns of microbial association networks in paddy soil within Eastern China
Xiaoling Wan,Qun Gao,Jianshu Zhao,Jiajie Feng,Joy D. Van Nostrand,Yunfeng Yang,Jizhong Zhou,Jizhong Zhou,Jizhong Zhou +8 more
TL;DR: This network analysis approach provided new insights into microbial community responses to environmental perturbations by inferring bacterial, fungal and diazotrophic associations across a large spatial scale in paddy soils.
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Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.
Yanying Zhang,Yanying Zhang,Qingsong Yang,Juan Ling,Joy D. Van Nostrand,Zhou Shi,Jizhong Zhou,Junde Dong +7 more
TL;DR: A comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangroves ecosystem.
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Exploring the accuracy of amplicon-based internal transcribed spacer markers for a fungal community.
Shuzhen Li,Shuzhen Li,Ye Deng,Zhujun Wang,Zhaojing Zhang,Zhaojing Zhang,Xiao Kong,Wenjun Zhou,Wenjun Zhou,Yanyun Yi,Yanyun Yi,Yuanyuan Qu +11 more
TL;DR: It was demonstrated that the three primer sets could not reach a consensus onFungal community composition or diversity, and that primer selection, not experimental treatment, determines observed soil fungal community diversity and composition.
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A miRNA181a/NFAT5 axis links impaired T cell tolerance induction with autoimmune type 1 diabetes
Isabelle Serr,Martin G. Scherm,Adam M. Zahm,Jonathan Schug,Victoria K. Flynn,Markus Hippich,Stefanie Kälin,Maike Becker,Peter Achenbach,Alexei Nikolaev,Katharina Gerlach,Nicole Liebsch,Brigitta Loretz,Claus-Michael Lehr,Benedikt Kirchner,Melanie Spornraft,Bettina Haase,James H. Segars,Christoph Küper,Ralf Palmisano,Ari Waisman,Richard A. Willis,Wan-Uk Kim,Wan-Uk Kim,Benno Weigmann,Klaus H. Kaestner,Anette Gabriele Ziegler,Carolin Daniel +27 more
TL;DR: Using T cells from children at an early stage of islet autoimmunity without clinical T1D, a microRNA181a–mediated increase in signal strength of stimulation and costimulation links nuclear factor of activated T cells 5 (NFAT5) with impaired tolerance induction and autoimmune activation.
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Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus.
Yan Li,Kun Wang,Bo Zhang,Qichao Tu,Qichao Tu,Yufei Yao,Bomiao Cui,Biao Ren,Jinzhi He,Xin Shen,Joy D. Van Nostrand,Jizhong Zhou,Wenyuan Shi,Liying Xiao,Changqing Lu,Xuedong Zhou +15 more
TL;DR: The team concluded that fungal community imbalance could affect the bacterial community in the saliva and the host immunity in the mucous membrane, thereby constituting a direct or indirect cause of the development of OLP.
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.