高通量测序微生物多样性流程.pptVIP

高通量测序微生物多样性流程;微生物多样性;;454 Data Format -- sff;mothur;基本分析流程：;Trim Unique -- 初步去杂;Align -- rRNA Database;Align -- Method;kmer;b. Pairwise alignment;c. Re-insert gaps;Screen -- 二次去杂 ; Start End NBases Ambigs Polymer NumSeqs Minimum: 1 10893 332 0 4 1 2.5%-tile: 7 10893 407 0 5 68 25%-tile: 8 10893 470 0 5 673 Median: 25 10893 485 0 6 1346 75%-tile: 45 10893 515 0 7 2019 97.5%-tile: 1036 12128 532 0 7 2624 Maximum: 2162 13980 555 0 7 2691 # of unique seqs: 2157 total # of seqs: 2691;Chimeric -- 去除嵌合 ;Distance – 计算距离; Nearest neighbor : Each of the sequences within an OTU are at most X% distant from the most similar sequence in the OTU. Furthest neighbor : All of the sequences within an OTU are at most X% distant from all of the other sequences within the OTU. Average neighbor : This method is a middle ground between the other two algorithms.;OTU —— ;Classify -- 分类学分析;mothur will find the 10 most similar sequences in the database. Once mothur has identified the k-most similar sequences, she will use the taxonomy information for each sequence to determine the consensus taxonomy. ;method=bayesian;HHBK7OF02GRRUS Bacteria{superkingdom}(100);Bacteroidetes{phylum}(100);Bacteroidia{class}(100);Bacteroidales{order}(100);Bacteroidaceae{family}(100);Bacteroides{genus}(100);unclassified; HHBK7OF02FVMOK Bacteria{superkingdom}(100);Firmicutes{phylum}(100);Clostridia{class}(100);Clostridiales{order}(100);Peptostreptococcaceae{family}(100);Peptostreptococcaceae_Incertae_Sedis(100);Peptostreptococcaceae_Incertae_Sedis_uncultured_Clostridium_sp.{species}(94);unclassified;;Classify -- 分类学分析;Rarefaction –稀释性曲线 ;Estimator –多样性指数;全样品相似度对比;非加权组平均法(unweighted pair-group method with arithmetic means, UPGMA);多样品相似度比较树;NEWICK is a standard format that is recognized by most programs that generate or allow visualization of phylogenetic trees including PHYLIP, TREE-PUZZLE, ARB, and TREEVIEW. ;FastTree;Heuristic neighbor-joining Reducing the length of the tree