测序原始数据分析——Mothur.docxVIP

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测序原始数据分析——Mothur.docx

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测序原始数据分析——Mothur

454 SOP NOTE:?Although this is an SOP, it is something of a work in progress and continues to be modified as we learn more. If you are using this protocol in a paper, you must cite the Schloss et al. 2011 PLoS ONE paper and cite the date you accessed this page: Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE. 6:e27310. This goal of this tutorial is to demonstrate the standard operating procedure (SOP) that the Schloss lab uses to process their 16S rRNA gene sequences that are generated by 454 pyrosequencing. Throughout the tutorial several alternative approaches will be mentioned along with why we might deviate from the SOP to use these approaches. This SOP is largely the product of a series of manuscripts that we have published and users are advised to consult these for more details and background data. The workflow is being divided into several parts shown here in the table of contents for the tutorial: Contents ?[ HYPERLINK /wiki/454_SOP hide]? HYPERLINK /wiki/454_SOP \l Logistics 1?Logistics HYPERLINK /wiki/454_SOP \l Getting_started 2?Getting started HYPERLINK /wiki/454_SOP \l Reducing_sequencing_error 3?Reducing sequencing error HYPERLINK /wiki/454_SOP \l Using_flowgrams 3.1?Using flowgrams HYPERLINK /wiki/454_SOP \l Using_quality_scores 3.2?Using quality scores HYPERLINK /wiki/454_SOP \l Processing_improved_sequences 4?Processing improved sequences HYPERLINK /wiki/454_SOP \l Removing_chimeras 5?Removing chimeras HYPERLINK /wiki/454_SOP \l Removing_.22contaminants.22 6?Removing contaminants HYPERLINK /wiki/454_SOP \l Error_analysis 7?Error analysis HYPERLINK /wiki/454_SOP \l Preparing_inputs_for_analysis 8?Preparing inputs for analysis HYPERLINK /wiki/454_SOP \l OTUs 8.1?OTUs HYPERLINK /wiki/454_SOP \l Phylotype 8.2?Phylotype HYPERLINK /wiki/454_SOP \l Phylogenetic_tree 8.3?Phylogenetic tree HYPERLINK /wik