2数量导入Importing微生物

# 激活工作环境
source activate qiime2-2017.8

# 建立工作目录
mkdir -p qiime2-importing-tutorial
cd qiime2-importing-tutorial

导入带品质值的测序数据

地球微生物组标准混样单端数据 “EMP
protocol” multiplexed single-end fastq

此类数据标准包蕴多少个文件,扩展名均为fastq.gz,三个是barcode文件,2个是样品混样测序文件。

# 建样品目录
mkdir -p emp-single-end-sequences

# 下载 barcode文件
wget -O emp-single-end-sequences/barcodes.fastq.gz https://data.qiime2.org/2017.8/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz

# 下载序列文件
wget -O emp-single-end-sequences/sequences.fastq.gz https://data.qiime2.org/2017.8/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz

# 导入QIIME2格式
qiime tools import \
  --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza

地球微生物组标准混样双端数据 “EMP
protocol” multiplexed paired-end fastq

此类数据标准蕴涵多少个公文,扩张名均为fastq.gz,3个是barcode文件,多个是样品混样测序文件。

# 建样品目录
mkdir -p emp-paired-end-sequences

# 下载序列正向和反向文件
wget -O emp-paired-end-sequences/forward.fastq.gz https://data.qiime2.org/2017.8/tutorials/atacama-soils/1p/forward.fastq.gz
wget -O "emp-paired-end-sequences/reverse.fastq.gz https://data.qiime2.org/2017.8/tutorials/atacama-soils/1p/reverse.fastq.gz

# 下载barcode文件
wget -O emp-paired-end-sequences/barcodes.fastq.gz https://data.qiime2.org/2017.8/tutorials/atacama-soils/1p/barcodes.fastq.gz

# 导入QIIME2格式
qiime tools import \
  --type EMPPairedEndSequences \
  --input-path emp-paired-end-sequences \
  --output-path emp-paired-end-sequences.qza

样品文件清单格式 “法斯特q manifest”
formats

# 下载fastq压缩包zip文件,其中的样品文件和清单文件mainfest
wget -O se-33.zip https://data.qiime2.org/2017.8/tutorials/importing/se-33.zip
wget -O se-33-manifest https://data.qiime2.org/2017.8/tutorials/importing/se-33-manifest
wget -O pe-64.zip https://data.qiime2.org/2017.8/tutorials/importing/pe-64.zip
wget -O pe-64-manifest https://data.qiime2.org/2017.8/tutorials/importing/pe-64-manifest
# 解压fastq样品文件
unzip -q se-33.zip
unzip -q pe-64.zip

样品清单是包含样品名、文件地点、文件方向三列的csv文件,以pe-64-manifest为例,内容如下:

# 样品名、文件位置、文件
sample-id,absolute-filepath,direction
sample1,$PWD/pe-64/s1-phred64-r1.fastq.gz,forward
sample1,$PWD/pe-64/s1-phred64-r2.fastq.gz,reverse
sample2,$PWD/pe-64/s2-phred64-r1.fastq.gz,forward
sample2,$PWD/pe-64/s2-phred64-r2.fastq.gz,reverse

导入品质值不相同编码的两类公事Phred3一半4
(一般Phred33微生物,正如普遍,唯有充足老的数据才有Phred64格式)

# 导入Phred33格式测序结果
qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path se-33-manifest \
  --output-path single-end-demux.qza \
  --source-format SingleEndFastqManifestPhred33
# 导入Phred64格式测序结果
qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path pe-64-manifest \
  --output-path paired-end-demux.qza \
  --source-format PairedEndFastqManifestPhred64

导入OTU表Biom文件

BIOM v1.0.0

# 下载数据并导入为QIIME2的qza格式
wget -O feature-table-v100.biom https://data.qiime2.org/2017.8/tutorials/importing/feature-table-v100.biom
qiime tools import \
  --input-path feature-table-v100.biom \
  --type 'FeatureTable[Frequency]' \
  --source-format BIOMV100Format \
  --output-path feature-table-1.qza

BIOM v2.1.0

wget -O feature-table-v210.biom https://data.qiime2.org/2017.7/tutorials/importing/feature-table-v210.biom
qiime tools import \
  --input-path feature-table-v210.biom \
  --type 'FeatureTable[Frequency]' \
  --source-format BIOMV210Format \
  --output-path feature-table-2.qza

代表性体系 Per-feature unaligned sequence
data

wget -O sequences.fna https://data.qiime2.org/2017.8/tutorials/importing/sequences.fna
qiime tools import \
  --input-path sequences.fna \
  --output-path sequences.qza \
  --type 'FeatureData[Sequence]'

多类别比对后的代表性种类导入(多连串比对后的种类中包含减号,表示比对的gap)
Per-feature unaligned sequence data

wget -O aligned-sequences.fna https://data.qiime2.org/2017.8/tutorials/importing/aligned-sequences.fna
qiime tools import \
  --input-path aligned-sequences.fna \
  --output-path aligned-sequences.qza \
  --type 'FeatureData[AlignedSequence]'

无根进化树导入 Phylogenetic trees
(unrooted)

wget -O unrooted-tree.tre https://data.qiime2.org/2017.8/tutorials/importing/unrooted-tree.tre
qiime tools import \
  --input-path unrooted-tree.tre \
  --output-path unrooted-tree.qza \
  --type 'Phylogeny[Unrooted]'

相关文章