DOC_ID : T11-0001
 

Doc_ID: A08-0001NCBIBioProj33317scikit0.24.1
Editor: Anita
Reviewer: 

Description

參考QIIME2 forum上的文章，使用RESCRIPt下載來自NCBI Genbank的序列和分類，並訓練適用於QIIME2分析的分類器。

Ref : https://forum.qiime2.org/t/using-rescript-to-compile-sequence-databases-and-taxonomy-classifiers-from-ncbi-genbank/15947

Source

Download URL : –

File size :

1. ncbi-refseqs-unfiltered.qza   198KB 
2. ncbi-refseqs-taxonomy-unfiltered.qza    19.1KB

Genome assemble version : BioProj33317

Detail information :

使用RESCRIPt下載來自NCBI Genbank的序列和分類，並訓練適用於QIIME2分析的classifiers，請確認已完成qiime2 standard analysis environment的安裝

#Activate standard analysis environment
conda activate qiime2
 

#移動到/work/使用者帳號資料夾
cd /work/u5777333/
 

#創建放置參考序列及相應的分類法文件的資料夾
mkdir -p NCBIclassifier/BioProject_33317
 

#移動至資料夾
cd NCBIclassifier/BioProject_33317
 

#安裝RESCRIPt
conda install -c conda-forge -c bioconda -c qiime2 -c defaults xmltodict

pip install git+https://github.com/bokulich-lab/RESCRIPt.git
 

# 使用RESCRIPt下載來自NCBI Genbank的序列和分類資料
qiime rescript get-ncbi-data \
    –p-query ‘33317[BioProject]’ \
    –o-sequences ncbi-refseqs-unfiltered.qza \
    –o-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza
 

#Filter unusually short 16S rRNA gene sequences
qiime rescript filter-seqs-length-by-taxon \
    –i-sequences ncbi-refseqs-unfiltered.qza \
    –i-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza \
    –p-labels Archaea Bacteria \
    –p-min-lens 900 1200 \
    –o-filtered-seqs ncbi-refseqs.qza \
    –o-discarded-seqs ncbi-refseqs-tooshort.qza
 

#using the –m-ids-to-keep-file parameter to only retain features found in our filtered sequences file
qiime rescript filter-taxa \
    –i-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza \
    –m-ids-to-keep-file ncbi-refseqs.qza \
    –o-filtered-taxonomy ncbi-refseqs-taxonomy.qza
 

#利用RESCRIPt來訓練classifiers
qiime rescript evaluate-fit-classifier \
    –i-sequences ncbi-refseqs.qza \
    –i-taxonomy ncbi-refseqs-taxonomy.qza \
    –o-classifier ncbi-refseqs-classifier.qza \
    –o-evaluation ncbi-refseqs-classifier-evaluation.qzv \
    –o-observed-taxonomy ncbi-refseqs-predicted-taxonomy.qza

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