基于Docker进行qiime2扩增子分析流程

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"

########################################################################

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

this results in a directory that has a nice summary in HTML

the heads of the reads are lower quality for bo