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Bacterial Antimicrobial Resistance annOtation of Genomes - Metagenomic Oxford Nanopore
***** Still Under Development *****

Report Bug · Request Feature

*see below sections for in-depth subworkflows

BALROG is a nextflow pipeline built to utilize Q20+ Oxford Nanopore Long-reads to investigate antimicrobial resistance (AMR) and its mobility from metagenomic samples. While looking at AMR is the main goal of BALROG, it also provides subworkflows for many related analysies, such as pathogen detection and metagenomic community analysis.

Not all features are fully implemented, and while the pipeline MIGHT work in its current state, I would fully expect some troubleshooting to be in store. If you do deciede to test it out in its current state please repot any and all bugs you find, or any suggestions for improvements!

Before you get too far along, familiarize youself with the section to make sure this is the pipeline for you, and that you can meet the requirements. (Don't worry, there isnt too much to do)

BALROG in its current form expects Q20+ Oxford Nanopore Long Read Metagenomic Sequecning. BALROG can run in Assembly-Free mode or assembles a metagenome using MetaFLYE, allowing for the analysis of low and high coverage metagenomes. BALROG in its standard configuration will require 100GB of RAM.

If you would like to run BALROG with older, non-Q20+ Nanopore data, feel free to submit a feature request and I will add the option.

All Dependicies are mannaged via Docker Containers and hosted on DockerHub. One of the following container runtime software packages will be required.

1. Nextflow (>= 23.04.0.5857) - Install Nextflow
2. Docker/Singularity/Apptainer - Install Docker - Install Singularity - Install Apptainer

Perfered Method - Download Release

wget https://github.com/edwardbirdlab/BALROG-MON/releases/download/v0.0.0/BALROG-0.0.0.tar.gz
tar -xzf BALROG-0.0.0.tar.gz

Method 2 - Clone Repo

git clone https://github.com/edwardbirdlab/BALROG-MON

BALROG takes a CSV (Comma-Seperted-Value) sheet as the input. Sample comlumn will be the prefix for all output files for that sample.
Example Format:

sample,path,refernce_genome
Sample_Name_1,/absolute/path/to/sample1.fastq.gz,/absolute/path/to/reference_genome_1.fna
Sample_Name_2,/absolute/path/to/sample2.fastq.gz,/absolute/path/to/reference_genome_1.fna

When crating a nextflow config ensure a container runtime is enabled (Singularity/Apptainer/Docker). If you are using slurm, you can use the incuded Beocat slurm config as a template. Most nf-core configs will also be supported. If you have never crated a nextflow config, or are having issues reach out to your local administraction.
Nextflow Configuration - nf-core configs

If you want to change any parameters from defualt they can be changed using the nextflow.config file. Configurable paramaters will be outlied in the detail sections below, as well as in the config file.

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1. Running the whole pipeline

nextflow run /path/to/edwardbirdlab/BALROG-MON -c /path/to/config.cfg

2. Optional: Pathogen Detection Conformation (NOT IMPLEMENTED YET)

nextflow run -resume /path/to/edwardbirdlab/BALROG-MON -c /path/to/config.cfg --taxid-list /path/to/taxid_list.txt

3. Optional: Multi-QC

nextflow run /path/to/edwardbirdlab/BALROG-MON -c /path/to/config.cfg --workflow-opt multiqc

1. Standardize Read Names - Included Python Script - (Optional step that is usefull if you have long read names)
2. Raw Read FastQC - FastQC
3. Porechop - PoreChop
4. Chopper - Chopper
   Params - params.chopper_minlen = (defualt = 500) - params.chopper_averagequality = (defualt = 20)
5. Trimed Read FastQC - FastQC

1. Mapping to Host Genome - Minimap2
2. Extracting Non-Host Reads Names - Samtools
3. Extract Non-Host Reads - SeqTK

1. Assembly:
   Assembly Free: Convert Fastq to Fasta - SeqTK
   OR
   Metagenomic Assembly - MetaFLYE

2. Plasmid Prediction - Plasmer Params - params.plasmer_min_len = (defualt = 500) - params.plasmer_max_len = (defualt = 500000)

3. Assembly QC - Quast

Multi AMR is run by defualt, however it can be switched to only run CARD by setting params.cardonly = TRUE

1. CARD
2. AMRFinder Plus
3. Resfinder

1. Kraken2
2. Bracken
3. Results ready to view in Pavian

1. Kraken2 - (--report-minimizer-data --minimum-hit-groups 3)
2. K2Verify - Comming soon! - (Not yet implemented)
3. Results ready to view in [Pavian](https://github.com/jenniferlu717/Bracken

1. MobileElementFinder

1. Kraken2

As there is currently no paper associated with BAROG-MON, please cite this Github page. Also, I feel free to contact me ([email protected] | [email protected]) to let me know!

Many tools are used in this pipeline, cite them according to their respective requrests. links are give above.

Distributed under the MIT License. See LICENSE for more information.

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Edward Bird - - [email protected] | [email protected]

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