Qiime2を使った微生物叢の解析（その３）

アライメントして系統樹を作成

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime alignment mafft --i-sequences rep-seqs-20180220_Kazusa.qza --o-alignment aligned-rep-seqs-20180220_Kazusa.qza

aligned-rep-seqs-20180220_Kazusa.qzaが保存されます。

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime alignment mask --i-alignment aligned-rep-seqs-20180220_Kazusa.qza --o-masked-alignment masked-aligned-rep-seqs-20180220_Kazusa.qza

masked-aligned-rep-seqs-20180220_Kazusa.qzaが保存されます。

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime phylogeny fasttree --i-alignment masked-aligned-rep-seqs-20180220_Kazusa.qza --o-tree unrooted-tree.qza

unrooted-tree.qzaが保存されます。

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime phylogeny midpoint-root --i-tree unrooted-tree.qza --o-rooted-tree rooted-tree.qza

rooted-tree.qzaが保存されます。

α、ß多様性の解析結果を出力

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table-20180220_Kazusa.qza --p-sampling-depth 7118 --m-metadata-file 20180220_Kazusa-metadata.tsv --output-dir core-metrics-7118-results

＊--p-sampling-depth には、depthの最小値を入れる。

以下のファイルが保存されます。

Saved FeatureTable[Frequency] to: core-metrics-7118-results/rarefied_table.qza
Saved SampleData[AlphaDiversity] % Properties(['phylogenetic']) to: core-metrics-7118-results/faith_pd_vector.qza
Saved SampleData[AlphaDiversity] to: core-metrics-7118-results/observed_otus_vector.qza
Saved SampleData[AlphaDiversity] to: core-metrics-7118-results/shannon_vector.qza
Saved SampleData[AlphaDiversity] to: core-metrics-7118-results/evenness_vector.qza
Saved DistanceMatrix % Properties(['phylogenetic']) to: core-metrics-7118-results/unweighted_unifrac_distance_matrix.qza
Saved DistanceMatrix % Properties(['phylogenetic']) to: core-metrics-7118-results/weighted_unifrac_distance_matrix.qza
Saved DistanceMatrix to: core-metrics-7118-results/jaccard_distance_matrix.qza
Saved DistanceMatrix to: core-metrics-7118-results/bray_curtis_distance_matrix.qza
Saved PCoAResults to: core-metrics-7118-results/unweighted_unifrac_pcoa_results.qza
Saved PCoAResults to: core-metrics-7118-results/weighted_unifrac_pcoa_results.qza
Saved PCoAResults to: core-metrics-7118-results/jaccard_pcoa_results.qza
Saved PCoAResults to: core-metrics-7118-results/bray_curtis_pcoa_results.qza
Saved Visualization to: core-metrics-7118-results/unweighted_unifrac_emperor.qzv
Saved Visualization to: core-metrics-7118-results/weighted_unifrac_emperor.qzv
Saved Visualization to: core-metrics-7118-results/jaccard_emperor.qzv
Saved Visualization to: core-metrics-7118-results/bray_curtis_emperor.qzv

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