QIIME 2 is a powerful, scalable, decentralized go microbiome analysis software package, emphasis on data analysis and transparent. QIIME 2 allows researchers to start from the original DNA sequence analysis, the level of direct access to statistical and pictures published results.
1. Install
Because before Miniconda already installed, this is not installed.
https://www.jianshu.com/p/eb89ab4af035
official installation documentation https://docs.qiime2.org/2019.1/install/
click Latest Docs , jump to https://docs.qiime2.org/2019.4/install / native /
latest version qiime2-2019.4-py36-linux-conda.yml
1.1 Download file
wget https://data.qiime2.org/distro/core/qiime2-2019.4-py36-linux-conda.yml
1.2 conda create environmental context name -n
conda env create -n qiime2-2019.4 --file qiime2-2019.4-py36-linux-conda.yml
1.3 optional step, just delete the downloaded file
rm qiime2-2019.4-py36-linux-conda.yml
1.4 activation conda environment, run
source activate qiime2-2019.4
1.5 Test
qiime --help
Did not report any error when you run this command, the installation was successful!
1.6 deactivate environment, run
source deactivate
2. Data Import
2.1 Overview about the required parameters and non-essential parameters
qiime tools import --help
Usage: qiime tools import [OPTIONS]
Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/
for usage examples and details on the file types and associated semantic
types that can be imported.
#导入数据以开始新的qiime 2工作。
#有关用法示例和可以导入的文件类型和相关语义的详细信息类型参见https://docs.qiime2.org/。
Options:
--type TEXT The semantic type of the artifact that will be
created upon importing. Use --show-importable-types
to see what importable semantic types are available
in the current deployment. [required]
--input-path PATH Path to file or directory that should be imported.
[required]
--output-path ARTIFACT Path where output artifact should be written.
[required]
--input-format TEXT The format of the data to be imported. If not
provided, data must be in the format expected by the
semantic type provided via --type.
--show-importable-types Show the semantic types that can be supplied to
--type to import data into an artifact.
--show-importable-formats
Show formats that can be supplied to --input-format
to import data into an artifact.
--help Show this message and exit.
Parameters must be entered is 3:
of the type, the INPUT-path, the Output-path
2.2 --type
Enter the following command to view the type of parameter type
qiime tools import --show-importable-types
Export
DeblurStats
DistanceMatrix
EMPPairedEndSequences
EMPSingleEndSequences
ErrorCorrectionDetails
FeatureData[AlignedSequence]
FeatureData[Importance]
FeatureData[PairedEndSequence]
FeatureData[Sequence]
FeatureData[Taxonomy]
FeatureTable[Balance]
FeatureTable[Composition]
FeatureTable[Frequency]
FeatureTable[PercentileNormalized]
FeatureTable[PresenceAbsence]
FeatureTable[RelativeFrequency]
Hierarchy
MultiplexedPairedEndBarcodeInSequence
MultiplexedSingleEndBarcodeInSequence
PCoAResults
Phylogeny[Rooted]
Phylogeny[Unrooted]
Placements
QualityFilterStats
RawSequences
SampleData[AlphaDiversity]
SampleData[BooleanSeries]
SampleData[ClassifierPredictions]
SampleData[DADA2Stats]
SampleData[FirstDifferences]
SampleData[JoinedSequencesWithQuality]
SampleData[PairedEndSequencesWithQuality]
SampleData[RegressorPredictions]
SampleData[SequencesWithQuality]
SampleData[Sequences]
SampleEstimator[Classifier]
SampleEstimator[Regressor]
TaxonomicClassifier
UchimeStats
2.3 --input-path
In addition to the requirements qiime2 fastq file, you also need a manifest file txt format.
#absolute filepaths “Fastq manifest” formats *file name: pe-33-manifest
sample-id,absolute-filepath,direction
SRR6025627,/media/luozhixin/0000678400004823/Qiime2/20190601/SRR6025627.1.clean.fastq.gz,forward
SRR6025627,/media/luozhixin/0000678400004823/Qiime2/20190601/SRR6025627.2.clean.fastq.gz,reverse
SRR6025635,/media/luozhixin/0000678400004823/Qiime2/20190601/SRR6025635.1.clean.fastq.gz,forward
SRR6025635,/media/luozhixin/0000678400004823/Qiime2/20190601/SRR6025635.2.clean.fastq.gz,reverse
After saving renamed pe-33-manifest
2.3 --output-path
The output file path and name of
the current path:
--output-path paired-end-demux.qza \
2.4 --input-format
Enter the following command to view the type of parameter format
qiime tools import --show-importable-formats
Divided PairedEndFastqManifestPhred33 and PairedEndFastqManifestPhred64
is actually Phred33 or Phred64.
2.5 Example
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path pe-33-manifest \
--output-path paired-end-demux.qza \
--input-format PairedEndFastqManifestPhred33
3.
Generating a visualization 3.1
qiime demux summarize \
--i-data paired-end-demux.qza \
--o-visualization paired-end-demux.qzv
--i-data, the input data; - o-visualization, the output file.
3.2 paired-end-demux.qzv visualization file
qiime tools view paired-end-demux.qzv
Press the 'q' key, Control-C, or Control-D to quit.
4 denoising, combined two-terminal sequence
4.1.1 denoising
qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 270 \
--p-trunc-len-r 250 \
--o-table table.qza \
--o-representative-sequences rep-seqs.qza \
--o-denoising-stats denoising-stats.qza \
--p-n-threads 0
parameter:
--i-demultiplexed-seqs # input file specified
--p-trim-left # cutting edge for the low mass region
--o-representative-sequences # output representative sequence
--pn-threads # CPU calling thread
4.1.2 generates the visualization
qiime metadata tabulate \
--m-input-file denoising-stats.qza \
--o-visualization denoising-stats.qzv
qzv files can be viewed online
4.2.1 Merge
qiime vsearch join-pairs \
--i-demultiplexed-seqs paired-end-demux.qza \
--o-joined-sequences joined.qza
4.2.2 generates the visualization
qiime demux summarize \
--i-data joined.qza \
--o-visualization joined.qzv
5. QC
qiime quality-filter q-score-joined
--i-demux joined.qza
--o-filtered-sequences joined-filtered.qza\
--o-filter-stats joined-filtered-stats.qza
qiime metadata tabulate
--m-input-file joined-filtered-stats.qza\
--o-visualization joined-filtered-stats.qzv
Reproduced in: https: //www.jianshu.com/p/1c2cce847581