qiime流程备忘

1.qiime1

1.1 给分好的序列改名成所需要的,使用python,shell不会这么简单的操作。。。:

# -*- coding: UTF-8 -*-
import os

for a in os.listdir('./'):
        if '_1_S0_L007_R2_001.fastq.gz' in a:
                fq1 = a
                fq2 = a.split('_1_S0_L007_R2_001.fastq.gz')[0] + '_2_S0_L007_R2_001.fastq.gz'
                name = a.split('_1_S0_L007_R2_001.fastq.gz')[0]
                cmd = 'fastp -f 24 -F 23 \
                 -i %s  -I %s -o primer_trimmed_fastqs/%s_1_S0_L007_R2_001.fastq.gz \
        -O primer_trimmed_fastqs/%s_2_S0_L007_R2_001.fastq.gz' % (fq1, fq2, name, name)
                os.system(cmd)

1.2 直接合并序列,有点简单粗暴,暂不确定科学性

import os

for a in os.listdir('./'):
    if '_1_S0_L007_R2_001.fastq.gz' in a:
        fq1 = a
        fq2 = a.split('_1_S0_L007_R2_001.fastq.gz')[0] + '_2_S0_L007_R2_001.fastq.gz'
        name = a.split('_1_S0_L007_R2_001.fastq.gz')[0]
        cmd = 'zcat %s* >> combine/%s_1_S0_L007_R1_001.fastq' % (name, name)
        os.system(cmd)

os.system('gzip combine/*')

1.3 进入qiime和usearch的流程,参考公众号宏基因组的教程推文

这里把导入数据的命令再次放在这:
multiple_split_libraries_fastq.py -i ./combine -o qiime1

1.4 画柱状组,看结果

2. qiime的继续测试

qiime2代表未来,一定要努力掌握,否则就跟不上时代,qiime2现在发布的版本已经足够可用了,加油学习!

2.1 导入数据

qiime tools import \
--type 'SampleData[SequencesWithQuality]' \
--input-path casava-18-single-end-demultiplexed \
--input-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path demux-single-end.qza

2.2 统计样本测序质量QC

qiime demux summarize \
  --i-data demux.qza \
  --o-visualization demux.qzv

2.3 质控和特征表构建(dada2)

qiime dada2 denoise-single   --i-demultiplexed-seqs demux-se.qza --p-trim-left 0  --p-trunc-len 126   --o-representative-sequences rep-seqs-dada2.qza   --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza

2.4

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