质控工具:DADA2, Deblur, basic quality-score-based filtering(任一个)
产出文件:FeatureTable[Frequency] 特征表 每个样品里面每个唯一序列的个数
FeatureData[Sequence] 特征数据 每个样品里面的唯一序列,跟特征表对应
示例1、
方法1:DADA2
qiime dada2 denoise-single \ --i-demultiplexed-seqs demux.qza \ --p-trim-left 0 \ (后面的数字表示从序列的第number位点开始截取,位点前面的舍弃,参考demux.qzv碱基质量) --p-trunc-len 120 \ (后面的数字表示截取结束位点,参考demux.qzv碱基质量) --o-representative-sequences rep-seqs-dada2.qza \ --o-table table-dada2.qza \ --o-denoising-stats stats-dada2.qza qiime metadata tabulate \ --m-input-file stats-dada2.qza \ --o-visualization stats-dada2.qzv mv rep-seqs-dada2.qza rep-seqs.qza mv table-dada2.qza table.qza
方法2:Deblur
qiime quality-filter q-score \ --i-demux demux.qza \ --o-filtered-sequences demux-filtered.qza \ --o-filter-stats demux-filter-stats.qza qiime deblur denoise-16S \ --i-demultiplexed-seqs demux-filtered.qza \ --p-trim-length 120 \ --o-representative-sequences rep-seqs-deblur.qza \ --o-table table-deblur.qza \ --p-sample-stats \ --o-stats deblur-stats.qza qiime metadata tabulate \ --m-input-file demux-filter-stats.qza \ --o-visualization demux-filter-stats.qzv qiime deblur visualize-stats \ --i-deblur-stats deblur-stats.qza \ --o-visualization deblur-stats.qzv
示例2、
DaDa2:
qiime dada2 denoise-single \ --p-trim-left 13 \ --p-trunc-len 150 \ --i-demultiplexed-seqs fmt-tutorial-demux-1.qza \ --o-representative-sequences rep-seqs-1.qza \ --o-table table-1.qza \ --o-denoising-stats stats-1.qza qiime dada2 denoise-single \ --p-trim-left 13 \ --p-trunc-len 150 \ --i-demultiplexed-seqs fmt-tutorial-demux-2.qza \ --o-representative-sequences rep-seqs-2.qza \ --o-table table-2.qza \ --o-denoising-stats stats-2.qza qiime feature-table merge \(合并不同处理组,不同于示例3的双端合并) --i-tables table-1.qza \ --i-tables table-2.qza \ --o-merged-table table.qza qiime feature-table merge-seqs \ --i-data rep-seqs-1.qza \ --i-data rep-seqs-2.qza \ --o-merged-data rep-seqs.qza
示例3、
DaDa2:
qiime dada2 denoise-paired \(DaDa2可以双端合并) --i-demultiplexed-seqs demux.qza \ --p-trim-left-f 13 \ --p-trim-left-r 13 \ --p-trunc-len-f 150 \ --p-trunc-len-r 150 \ --o-table table.qza \ --o-representative-sequences rep-seqs.qza \ --o-denoising-stats denoising-stats.qza