基于Docker进行qiime2扩增子分析流程_qiime2 docker分析扩增子-优快云博客

本文档详细记录了基于Docker的qiime2进行扩增子数据分析的过程，包括数据获取、单线程处理、质量控制、特征表生成、系统发育树构建、多样性和相关性分析等步骤。特别地，提到了--p-sampling-depth参数的重要性和处理连续元数据的考虑，以及在处理pH值时遇到的挑战。

get data

wget -O "sample-metadata.tsv" \
  	"https://data.qiime2.org/2020.2/tutorials/atacama-soils/sample_metadata.tsv"

mkdir emp-paired-end-sequences

wget -O "emp-paired-end-sequences/forward.fastq.gz" \
  	"https://data.qiime2.org/2020.2/tutorials/atacama-soils/10p/forward.fastq.gz"

wget -O "emp-paired-end-sequences/reverse.fastq.gz" \
  	"https://data.qiime2.org/2020.2/tutorials/atacama-soils/10p/reverse.fastq.gz"

wget -O "emp-paired-end-sequences/barcodes.fastq.gz" \
  	"https://data.qiime2.org/2020.2/tutorials/atacama-soils/10p/barcodes.fastq.gz"

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export WORK_DIR="/home/wkg/repos/qiime2/atacama"

docker run -t -i -v $WORK_DIR:/data qiime2/core:2020.2 \
	qiime tools import \
	--type EMPPairedEndSequences \ 
	--input-path emp-paired-end-sequences \ 
	--output-path emp-paired-end-sequences.qza

single thread

demux

docker run -t -i -v $WORK_DIR:/data qiime2/core:2020.2 \
	qiime demux emp-paired \
	--m-barcodes-file sample-metadata.tsv \ 
	--m-barcodes-column barcode-sequence \ 
	--p-rev-comp-mapping-barcodes \ 
	--i-seqs emp-paired-end-sequences.qza \ 
	--o-per-sample-sequences demux.qza \
	--o-error-correction-details demux-details.qza

single threaded

takes awhile

docker run -t -i -v $WORK_DIR:/data qiime2/core:2020.2 \
	qiime demux summarize \
	--i-data demux.qza \
	--o-visualization demux.qzv

single threaded. fast

to look at the visualizations and summary tables from the demux:

docker run -t -i -v $WORK_DIR:/data qiime2/core:2020.2 \
	qiime tools export \
	--input-path demux.qzv \
	--output-path demux_results

基于Docker进行qiime2扩增子分析流程