This repository is a modified version of the AMR++ core repository with some notable modifications, changes, and parameterised for running on Cardiff University Biosciences compute cluster (Trinity). For usage and tutorials refer to the core AMR++ documentation.

Notable changes to original pipeline:

• Integrated fastp & bowtie2 as QC and alignment packages
  • Note: Default alignment for megares is kept as BWA consistent with original AMR++ and can be changed by parameter. Bowtie2 alignment against megaresDB has significant change on alignment rate.
• Based upon modified docker image (passdan/amrplusplus-update)
• Some code tweaks and fixes to work with singularity-slurm submission and repair nextflow channel bugs
• Bespoke job submission and result caputre to fit our specific requirements
• Added Bracken processing with new results
  • Note: Two new workflow parameters: 'standard_AMR_wKraken_and_bracken' and 'kraken_and_braken' (for already filtered/host removed input)

Codebase is provided as-is and is hyper-locally modified for our infrastructure. If you are not concerned about bracken output or fastp & bowtie2 you probably want to work from the original AMR++ repository.

1. Download the github repository with git clone and the url above

2. The pipeline is designed and configured to run with singularity & slurm. If you are using these then no further installation preparation is required. You may choose to pre-build the singulariy images in advance if wanted. Note: config/singularity_slurm.conf is where singularity images can be defined.

3. Either download directly, or build your indexes to be filtered against from user supplied fasta files.

[Recommended] download human genome indexes directly from: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml

4. An example slurm script defines these parameters:
   • workdir: Location where processing will be performed (advice: use high speed location on your processing node i.e. /tmp)
   • installdir: Location of this github repo on your system
   • resultsdir: Where do you want the main outputs to be transfered to (not the full working folders & outputs)
   • run: Name of the run for annotation and folder where the fastq files are Default input read location is: $workdir/$run/fastq

Default pipeline is standard_AMR_wKraken_and_bracken which will run from raw fastqs to the endpoint. Alternatives are to use mid-process data, kraken only etc. by modifying the --pipeline parameter

Available pipelines:
    - demo: Run a demonstration of AMR++
    - standard_AMR: Run the standard AMR++ pipeline
    - fast_AMR: Run the fast AMR++ pipeline without host removal.
    - standard_AMR_wKraken: Run the standard AMR++ pipeline with Kraken
    - **NEW** standard_AMR_wKraken_and_bracken: Run the standard AMR++ pipeline with Kraken AND Bracken

Available subworkflows:
    - eval_qc: Run FastQC analysis
    - trim_qc: Run trimming and quality control
    - rm_host: Remove host reads
    - resistome: Perform resistome analysis
    - align: Perform alignment to MEGARes database
    - kraken: Perform Kraken analysis
    - **NEW** kraken_and_bracken: Perform Kraken and Bracken analysis
    - qiime2: Perform QIIME 2 analysis
    - bam_resistome: Perform resistome analysis on BAM files

Submit as a slurm & singularity job with:

sbatch AMRplusplus_full.sh

You're finished!