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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Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China
Ke Ma,Anzhou Ma,Guodong Zheng,Ge Ren,Fei Xie,Hanchang Zhou,Jun Yin,Yu Liang,Xuliang Zhuang,Guoqiang Zhuang +9 more
TL;DR: Zhang et al. as discussed by the authors used high-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity.
Posted ContentDOI
Read trimming has minimal effect on bacterial SNP calling accuracy
TL;DR: It is concluded that read quality- and adapter-trimming add relatively little value to a SNP calling pipeline and may only be necessary if small differences in the absolute number of SNP calls are critical.
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Contrasting responses of fungal and bacterial communities to biogas slurry addition in rhizospheric soil of poplar plantations
TL;DR: In this paper , the authors investigated the effects of biogas slurry application at different concentrations (Control, no treatment; Low, 250 m3 ha−1 yr−1; High, 375 m3 h−1 yr−1 ) on the microbial community structures in the rhizospheric soil of poplar plantations.
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Soil microbial community assembly and stability are associated with potato (Solanum tuberosum L.) fitness under continuous cropping regime
TL;DR: In this paper , a new index named cohesion tools were used to calculate the stability and complexity of soil microbial communities from eight potato cultivars grown under a continuous cropping regime by using the high-throughput sequencing data.
Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains
TL;DR: This dissertation conducted computational comparative genomics experiments with a panel of 20 of the most abundant Pseudomonas aeruginosa strains to enable direct comparison of the pathogenic potential of clinical and environmental strains and identification of their possible characteristic differences.
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.