SMURF使用经验

Bioinfoer

已于 2023-08-10 19:51:45 修改

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文章标签：大数据 github

于 2023-07-14 14:06:45 首次发布

本文链接：https://blog.csdn.net/xiaozheng1213/article/details/131716206

版权

5R 16S比对软件SMURF，官方网址NoamShental/5R at v1.0 (github.com)

下载安装SMURF

git clone https://github.com/NoamShental/5R.git
# 安装MCR
wget https://ssd.mathworks.com/supportfiles/downloads/R2019b/Release/4/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2019b_Update_4_glnxa64.zip
unzip MATLAB_Runtime_R2019b_Update_4_glnxa64.zip
./install
# 手动选择安装位置

最后可以把MCR安装位置添加到环境变量，也可以临时指定

On the target computer, append the following to your LD_LIBRARY_PATH environment variable:  /public/v97/runtime/glnxa64:/public/v97/bin/glnxa64:/public/v97/sys/os/glnxa64:/public/v97/extern/bin/glnxa64  If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable.

最后试一下示例数据

./5R_linux/run_main_5R.sh /public/v97 ./example_fastq ./GG_5R GreenGenes_201305 ./example_results/5R_SMURF_example.txt 126

Input params are:
Working on files in directory: ./example_fastq
Reconstruction using kmers of length: 126
WORKING ON SAMPLE 3: RDB123_ATGAGTGC
Part 1/1 - Block 1/2
Part 1/1 - Block 2/2
Number of reads: 231943
Percent of long enough reads: 1
Percent of good reads: 0.95891
Counting fasta write: 1
Elapsed time is 2.579405 seconds.
Mapped to primers 88% of unique reads
Mapped to primers 98% of read counts
Loading bacterial DB for region 1 out of 5 from original region 1
Loading bacterial DB for region 2 out of 5 from original region 2
Loading bacterial DB for region 3 out of 5 from original region 3
Loading bacterial DB for region 4 out of 5 from original region 4
Loading bacterial DB for region 5 out of 5 from original region 5
Region 1 out of 5
Keep high freq: 25% of reads
Keep high freq: 95% of counts
Building matrix M
Building matrix A
--------------------------------------------

阔以了

Two files are created:

results_filename.txt - A table of species' relative abundances (rows) in each sample (columns).

ReadCountStats_results_filename.txt - General statistics of the number reads that passed the quality filter, the number of reads matched to each regions etc.

突然发现这个流程输出结果没有ASV信息，我看这个干嘛呀，骂骂咧咧！！！！

好像q2-Sidle也可以比对，我去看看有没有，链接：

Welcome to Sidle — q2-sidle 2020.8 documentation