Ampliconsuite-pipeline

Introduction

AmpliconSuite-pipeline is an end-to-end wrapper around AmpliconArchitect (AA) and AmpliconClassifier (AC) for detecting and classifying focal copy number amplifications, such as ecDNA and BFBs, from paired-end whole genome sequencing data. Release 1.6.0 is a coordinated release of AA v1.6.r0, AC v2.0.0 and BFBArchitect v1.0.1. Supported reference builds: hg19, GRCh37, GRCh38 (hg38), GRCh38_viral, mm10. Image provenance Built at RCAC on 2026-08-13 from AmpliconSuite-pipeline/singularity/ ampliconsuite-pipeline.def, with Bootstrap changed from library to docker and symlinks added to expose the driver scripts on PATH. The upstream def pulls master/main branch archives rather than release tags, so this image is a branch snapshot taken shortly after the v1.6.0 release, not a tagged build. Run ‘AmpliconSuite-pipeline.py -v’ to see the versions actually installed. Reference annotations AA_DATA_REPO points at a shared, read-only site copy under /depot/itap/datasets/ampliconsuite/data_repo. Because that copy is not writable, AA cannot cache per-BAM coverage statistics into it. Pass –no_cstats, or point AA_DATA_REPO and APPTAINERENV_AA_DATA_REPO at your own writable copy. The site copy tracks ‘current’, which is repointed as new annotation snapshots are staged. If you need results reproducible against a fixed snapshot, set AA_DATA_REPO to the dated directory instead. Optimization solvers No commercial solver license is required. AA falls back to Clarabel and BFBArchitect falls back to CBC. Pass –AA_solver clarabel to skip Mosek detection entirely. If you hold a personal academic Mosek license, the container looks for it at /home/mosek/ inside the container, which is NOT your home directory. Bind it: export APPTAINER_BIND”$HOME/mosek:/home/mosek” Typical usage AmpliconSuite-pipeline.py -s SAMPLE -t 12 –bam sample.cs.bam –ref GRCh38 –AA_solver clarabel –no_cstats –run_AA –run_AC -o $CLUSTER_SCRATCH/ampliconsuite_out AmpliconArchitect itself is largely serial. The -t value drives BWA, CNVkit and samtools during data preparation, so a full-node request will sit idle through the AA stage. BAMs should be coordinate sorted and BWA-MEM aligned (do not set -m) against a supported build. BAMs pulled from SRA are frequently stripped of tags that AA needs to call breakpoints correctly.

For more information, please check:
Home page: https://github.com/AmpliconSuite/AmpliconSuite-pipeline
Guide: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/blob/master/documentation/GUIDE.md

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

GAUTSCHI

1.6.0

NEGISHI

1.6.0

Commands

  • AmpliconSuite-pipeline.py

  • GroupedAnalysisAmpSuite.py

  • AmpliconArchitect.py

  • amplified_intervals.py

  • amplicon_classifier.py

  • make_results_table.py

  • feature_similarity.py

  • BFBArchitect.py

  • BFBArchitect-batch

  • BFBArchitect-call-cnv

  • cnvkit.py

  • CAMPER.py

  • breakpoints_to_bed.py

  • convert_cns_to_bed.py

  • cycles_to_bed.py

  • graph_cleaner.py

  • graph_to_bed.py

  • plot_cnv_distribution.py

  • bfb_foldback_detection.py

  • integration_detection.py

  • readclust.py

Module

You can load the modules by:

module load biocontainers
module load ampliconsuite-pipeline

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run ampliconsuite-pipeline on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ampliconsuite-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ampliconsuite-pipeline

# Your ampliconsuite-pipeline workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ampliconsuite-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ampliconsuite-pipeline

# Your ampliconsuite-pipeline workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ampliconsuite-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ampliconsuite-pipeline

# Your ampliconsuite-pipeline workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ampliconsuite-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ampliconsuite-pipeline

# Your ampliconsuite-pipeline workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ampliconsuite-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers ampliconsuite-pipeline

# Your ampliconsuite-pipeline workflow...