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megagenomics分析方法与工具的文章
肖斌 2016-2-19 09:20
文章: Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes 2016 ( https://www.ncbi.nlm.nih.gov/pubmed/27067514 ) 文章: MetaCRAM: an integrated pipeline for metagenomic taxonomy identi ...
个人分类: 科研文章|5402 次阅读|没有评论
16s的分析流程文章总结
肖斌 2016-1-25 09:23
Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface 2013 ( http://www.ncbi.nlm.nih.gov/pubmed/23871656 ) Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amp ...
个人分类: 科研文章|3073 次阅读|没有评论
宏基因组DNA的提取
肖斌 2016-1-25 09:10
Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags 2013 ( http://www.ncbi.nlm.nih.gov/pubmed/23899773 )
个人分类: 科研文章|2941 次阅读|没有评论
python与内容提取
肖斌 2016-1-22 09:17
python实践,提取文章摘要: http://python.jobbole.com/83839/
个人分类: python|2109 次阅读|没有评论
metastats的使用
肖斌 2016-1-21 21:54
对于16s的数据,为了分析在不同group中丰度差异显著的菌群,2009年出现了工具Metastats( Metastats: an improved statistical method for analysis of metagenomic data),本文对此工具的用法进行了简单阐述。 第一,此工具提供了web服务,详见 http://metastats.cbcb.umd.edu/detect ...
个人分类: 科研文章|11849 次阅读|没有评论
嵌合体的研究文章总结
肖斌 2016-1-19 10:21
CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies 2015 ( http://www.ncbi.nlm.nih.gov/pubmed/25527546 )
个人分类: 工具mothur|1969 次阅读|没有评论
16s 研究方法的文章讨论
肖斌 2016-1-19 09:48
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies 2015 ( http://www.ncbi.nlm.nih.gov/pubmed/25880246 ) 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions 2015 ( http://www.ncbi.nlm.nih.gov/pubmed/25808518 ...
个人分类: 科研文章|2284 次阅读|没有评论
16s不同测序平台的文章总结
肖斌 2016-1-18 09:19
文章: A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling 2016 ( http://www.ncbi.nlm.nih.gov/pubmed/26763898 ) 文章: Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering ...
个人分类: 科研文章|3616 次阅读|没有评论
基于16s数据的功能注释文章总结
肖斌 2016-1-18 09:14
Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets 2016 ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746064/ ) A n integrated strategy for functional analysis of microbial communities based on gene ontology and ...
个人分类: 科研文章|2999 次阅读|没有评论
16s taxonomic assignment的研究文章总结
肖斌 2016-1-14 10:27
文章: Studying long 16S rDNA sequences with ultrafast- metagenomic sequence classification using exact alignments (Kraken) 2016 ( https://www.ncbi.nlm.nih.gov/pubmed/26812576 ) 文章: A novel semi-supervised algorithm for the taxonomic assignment of metagenomic re ...
个人分类: 科研文章|2669 次阅读|没有评论

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