AmpliconSuite

Wrapping the Amplicon Architect workflow:

1. Starts with PrepareAA
2. Loads PrepareAA results into Amplicon Architect
3. Loads Amplicon Architect results into Amplicon Classifier.

Licenses

The modules wrapped in AmpliconSuite-pipeline use the following licenses. Please note that the AmpliconArchitect license specifies that AmpliconArchitect is for research use and does not give license for commerical for-profit use.

AmpliconSuite-pipeline license (BSD 2-Clause)
AmpliconArchitect license (University of California software license)
AmpliconClassifier license (BSD 2-Clause)

Other dependencies used by these modules (e.g. Mosek, samtools, etc.) have their own set of licensing requirements which users should make themselves aware of as needed. The Mosek license requires that users obtain a copy (which is free for academic use) from the Mosek website. More information is available in the installation section.

Source Code

Prepare AA: https://github.com/jluebeck/PrepareAA
Amplicon Architect: https://github.com/jluebeck/AmpliconArchitect
Amplicon Classifier: https://github.com/jluebeck/AmpliconClassifier

Running Locally

• If you wish to run this module as a Docker container locally, here are the steps:

1. Pull the Docker image
   • docker pull genepattern/amplicon-architect
   • visit https://hub.docker.com/repository/docker/genepattern/amplicon-architect for versions
2. Start running using 'docker run', REQUIRED flags are required.
   • docker run genepattern/amplicon-architect:*version tag* python3 run_aa.py
     REQUIRED: --input ENTER FILEPATH TO INPUTS HERE (TWO FAST Q FILES, OR ONE BAM, OR ONE COMPLETED AA RUN)
     REQUIRED: --n_threads ENTER THE NUMBER OF THREADS TO USE
     REQUIRED: --reference ENTER THE REFERENCE GENOME, CHOICES: hg19, GRCh37, GRCh38, hg38, mm10, GRCm38
     REQUIRED: --file_prefix ENTER THE FILE PREFIX FOR OUTPUTS
     REQUIRED: --RUN_AA RUN AA AFTER ALIGNMENT, CHOICES: Yes, No
     REQUIRED: --RUN_AC RUN AC AFTER AA, Choices: Yes, No
     --ploidy SPECIFY PLOIDY
     --purity SPECIFY PURITY
     --cnvkit_segmentation CHOOSE CNVKIT SEGMENTATION TYPE, CHOICES: cbs, haar, hmm, hmm-tumor, hmm-germline, none.
     --AA_seed SPECIFY THE SEED USED FOR AA
     --cnv_bed FILEPATH TO BED FILE
     --metadata FILEPATH TO METADATA JSON FILE
     --normal_bam If the bam file provided is sorted or normal. Choices: Yes, No
     
   • Example run script:
     docker run genepattern/amplicon-architect:v2.11 python3 run_aa.py --input /home/user/edwin5588/SRR8788972_1.fastq /home/user/edwin5588/SRR8788972_2.fastq --n_threads 4 --reference GRCh38 --file_prefix SRR8788972 --RUN_AA Yes --RUN_AC Yes
   • Example run script using Docker, mounting a local data directory:
     docker run -v /local_data:/mount_dir genepattern/amplicon-architect:v2.4 python3 run_aa.py --input /mount_dir/SRR8788972_1.fastq /mount_dir/SRR8788972_2.fastq --n_threads 4 --reference GRCh38 --file_prefix SRR8788972 --RUN_AA Yes --RUN_AC Yes
3. Running using singularity:
   • Running the Docker image using Singularity is similar to the steps above, simply create an .sif file from the Docker tag:
     
     • Example: singularity pull -F --disable-cache docker://genepattern/amplicon-architect:v2.4
   • Next, run Amplicon Suite using Singularity. The arguments are the same as listed above.
     
     • Example run using Singularity: singularity exec amplicon-architect_v2.4.sif python3 /opt/genepatt/run_aa.py --input /home/user/edwin5588/SRR8788972_1.fastq /home/user/edwin5588/SRR8788972_2.fastq --n_threads 4 --reference GRCh38 --file_prefix SRR8788972 --RUN_AA Yes --RUN_AC Yes
     • Example run using Singularity, mounting a local data directory:
       singularity exec --bind /local_data:/mount_dir amplicon-architect_v2.4.sif python3 /opt/genepatt/run_aa.py --input /mount_dir/SRR8788972_1.fastq /mount_dir/SRR8788972_2.fastq --n_threads 4 --reference GRCh38 --file_prefix SRR8788972 --RUN_AA Yes --RUN_AC Yes

Dependencies and Versioning

• Uses Docker Image: genepattern/amplicon-architect:v2.11
• python 3.9

Contact

• Edwin Huang: edh021@cloud.ucsd.edu