因为我是双端数据，所以这一步我主要是参考了这个实战：
https://docs.qiime2.org/2018.2/tutorials/atacama-soils/
我前一步已经拿到了我切过引物的数据，要先看一下这个质量分布
这里我先上代码
qiime dada2 denoise-paired \
--p-n-threads 0 \
--i-demultiplexed-seqs trimmed-seqs.qza \
--o-table table \
--o-representative-sequences rep-seqs \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 220 \
--p-trunc-len-r 220
别忘了设置线程数哦
根据自己的分析需要来选择左边和右边切多少
我这里粗暴地切了220，切多切少都不好，要看你reads的具体质量
这一步其实很关键，会生成一个table 和一个 rep-seqs
用来做后续的分析
接下来就可以可视化 table 和 rep-seqs
qiime feature-table summarize \
--i-table table.qza \
--o-visualization table.qzv \
--m-sample-metadata-file sample-metadata.tsv
qiime tools view table.qzv
做table的时候要输入一个 sample-metadata.tsv 里面会有很多信息，后续分析也要用
qiime feature-table tabulate-seqs \
--i-data rep-seqs.qza \
--o-visualization rep-seqs.qzv
qiime tools view rep-seqs.qzv
这里我举一个之前失败的例子
这里sequence count 几乎没有。后面无法分析下去
建树
这一步基本就是看攻略
https://docs.qiime2.org/2018.2/tutorials/moving-pictures/
中文版的更好理解一点：https://blog.csdn.net/woodcorpse/article/details/75204871
perform a multiple sequence alignment of the sequences
qiime alignment mafft \
--i-sequences rep-seqs.qza \
--o-alignment aligned-rep-seqs.qza
Next, we mask (or filter) the alignment to remove positions that are highly variable. These positions are generally considered to add noise to a resulting phylogenetic tree.
qiime alignment mask \
--i-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza
Next, we’ll apply FastTree to generate a phylogenetic tree from the masked alignment.
qiime phylogeny fasttree \
--i-alignment masked-aligned-rep-seqs.qza \
--o-tree unrooted-tree.qza
we apply midpoint rooting to place the root of the tree at the midpoint of the longest tip-to-tip distance in the unrooted tree.
qiime phylogeny midpoint-root \
--i-tree unrooted-tree.qza \
--o-rooted-tree rooted-tree.qza
我这也是照葫芦画瓢
还是应该好好理解一番
