First, open your terminal. Then, run these two command lines :
cd -place_in_your_local_computer
git clone https://github.com/PLStenger/MADCAPS_NGS.git
git pull
cd 99_softwares/
conda install -c bioconda fastqc
conda install -c bioconda trimmomatic
conda install -c bioconda multiqc
For install QIIME2, please refer to http://qiime.org/install/install.html
sysctl hw.ncpu
> hw.ncpu: 4
# Put you in your working directory
cd /scratch_vol1/fungi/Coral_block_colonisation/00_scripts
# For run all pipeline, lunch only this command line :
time nohup bash 000_run_all_pipeline_in_one_script.sh &> 000_run_all_pipeline_in_one_script.out
# For run pipeline step by step, lunch :
# Run the first script for check the quality of your data and then for choosing the good cleanning parameters
time nohup bash 01_quality_check_by_FastQC.sh &> 01_quality_check_by_FastQC.out
real 2m29.904s
user 3m14.842s
sys 0m14.673s
# Go out of the folder
cd ..
# Go in the "02_quality_check" folder
cd 02_quality_check
# Run multiqc for synthetized information
multiqc .
# Go out of the folder
cd ..
# Go in the script folder
cd 00_script
# Run the second script for cleaned your data
time nohup bash 02_trimmomatic_q30.sh &> 02_trimmomatic_q30.out
real 1m12.017s
user 1m31.466s
sys 0m8.983s
# Run the third script for checking the quality of your cleaned data
time nohup bash 03_check_quality_of_cleaned_data.sh &> 03_check_quality_of_cleaned_data.out
real 5m5.974s
user 5m42.971s
sys 0m27.492s
# Go out of the folder
cd ..
# Go in the "04_quality_check" folder
cd 04_quality_check
# Run multiqc for synthetized information
multiqc .
# Go out of the folder
cd ..
# Go in the script folder
cd 00_script
# Try to deal with the V1V3 - V3V4 situation :
time nohup bash 04_fastq-cat.sh &> 04_fastq-cat.out
real 0m1.264s
user 0m0.039s
sys 0m0.692s
# Import the data in QIIME2 format
time nohup bash 05_qiime2_import_PE.sh &> 05_qiime2_import_PE.out
real 1m56.160s
user 0m55.588s
sys 0m11.154s
# Run the Denoise
time nohup bash 06_qiime2_denoise_PE.sh &> 06_qiime2_denoise_PE.out
real 66m29.579s
user 129m35.661s
sys 4m17.156s
# Run the tree construction
time nohup bash 07_qiime2_tree_PE.sh &> 07_qiime2_tree_PE.out
real 8m29.501s
user 2m23.194s
sys 0m20.178s
# Run the rarefaction
time nohup bash 08_qiime2_rarefaction_PE.sh &> 08_qiime2_rarefaction_PE.out
real 1m15.788s
user 0m28.194s
sys 0m8.118s
# For obtainning better plots, run this script on your computer :
08_qiime2_rarefaction_PE_plots.R
time nohup bash 09_qiime2_calculate_and_explore_diversity_metrics_PE.sh &> 09_qiime2_calculate_and_explore_diversity_metrics_PE.out
real 59m0.552s
user 7m23.905s
sys 1m51.603s
time nohup bash 10_qiime2_assign_taxonomy_PE.sh &> 10_qiime2_assign_taxonomy_PE.out
real 82m44.469s
user 74m58.003s
sys 1m21.506s
time nohup bash 11_core_biom_PE.sh &> 11_core_biom_PE.out
Run "12_FunGuild.sh" localy please
time nohup bash 13_PICRUSt2.sh &> 13_PICRUSt2.out
time nohup bash 99_junk.sh &> 99_junk.out