Bacterial Antimicrobial Resistance annOtation of Genomes - ISOlate whole genome

Report Bug · Request Feature

BALROG-ISO (Bacterial Antimicrobial Resistance annOtation of Genomes - ISOlate whole genome) is a comprehensive high throughput Nextflow pipeline built to utilize next generaion short-reads for the investigation of bacterial antimicrobial resistance (AMR) and its mobility from whole genome sequences of bacterial isolates. While AMR characterization is the main goal of BALROG-ISO, it also provides the taxonomic classification, gene identities, and assignment of gene origin (i.e. plasmid or chromosome) for the submitted isolate(s).

BALROG-MSR: Bacterial Antimicrobial Resistance annOtation of Genomes - Metagenomic Short Read
BALROG-MON: Bacterial Antimicrobial Resistance annOtation of Genomes - Metagenomic Oxford Nanopore

*See sections below for details on subworkflows

• Getting Started
• Running BALROG-ISO
• Core Steps of Workflow
• Citations
• License
• Contact Information

(back to top)

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

BALROG-ISO in its current form expects Illuminia/Aviti paired-end, short-read data. BALROG-ISO in its standard configuration will require 100GB of RAM.

All dependencies are managed via Docker Containers and hosted on DockerHub. In addion to Nextflow, one of the following container runtime software packages will be required:

• Nextflow (>= 23.04.0.5857) - Install Nextflow
• Docker/Singularity/Apptainer - Install Docker - Install Singularity - Install Apptainer

Preferred Method - Download Release

wget https://github.com/edwardbirdlab/BALROG-ISO/archive/refs/tags/1.0.0.tar.gz
tar -xzf 1.0.0.tar.gz

Method 2 - Clone Repo

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

BALROG-ISO takes a CSV (Comma-Seperated-Value) sheet as the input. Note that the "sample" column will be the prefix of all output files for that sample. This version does not automatically combine reads of the same sample name, so please combine sequencing runs manually before starting the pipeline.

Example Format:

sample,r1,r2
Sample_Name_1,/absolute/path/to/sample1_R1.fastq.gz,/absolute/path/to/sample1_R2.fastq.gz
Sample_Name_2,/absolute/path/to/sample2_R1.fastq.gz,/absolute/path/to/sample2_R2.fastq.gz

When creating 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 created a Nextflow config, or are having issues, reach out to your local administration.
Nextflow Configuration - nf-core configs

If you want to change any parameters of BALROG-ISO from its default options, they can be changed using the "nextflow.config" file, or via command line. Configurable parameters will be outlined in the detailed sections below, as well as in the config file.

Required Parameters

--samplesheet /path/to/samplesheet
--run_name "NameOfRun"

Optional Parameters

--sequencing_adapter_type illumina

Defines which adapter set to use.
Default: illumina (options = illumina, aviti, custom)

--custom_sequencing_adapter_r1 "ATGCATGC"

Sequence of the read 1 adapter.
Default: NaN

--custom_sequencing_adapter_r2 "ATGCATGC"

Sequence of the read 2 adapter.
Default: NaN

--fastp_minlen 100

The minimum read length.
Default: 100

--fastp_q 20

The minimum q-score threshold.
Default: 20

--busco_lineage bacteria_odb10

Sets which BUSCO lineage to use. Recommend changing if you have an expected taxon.
Default: bacteria_odb10

--params.plasmer_min_len = 500

Sets the minimum sequence length to be included in plasmid prediction. Not recommended to lower below 500.
Default = 500

-- params.plasmer_max_len = 500000

Sets the sequence length above which longer sequences are automatically predicted to be chromosomal in origin.
Default = 500000

--amrfinder_lineage Escherichia

Enables species-specific models in AMRFinderPlus. See AMRFinder documentation for supported species and how to supply the name of them.
Default: NaN

--resfinder_lineage "Escherichia coli"

Enables species-specific models in ResFinder. See ResFinder documentation for supported species and how to supply the name of them.
Default: NaN

(back to top)

1. Running the Whole Pipeline

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

2. Generate Multi-QC

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

(back to top)

Raw QC

• FastQC : Raw Read

Human Read Removal Tool

• sra-human-scrubber : Masks human sequences in data

Trimming

• fastp

Final QC

• FastQC : Trimmed Read

Genome Assembly

• SPAdes

Assembly Stats

• QUAST : Assembly Metrics Report

Genome Completeness

• BUSCO: Single-Copy Ortholog "Completeness"

• GTDB-Tk

Sequence Origin Assignment

• Plasmer : Plasmid prediction
  

Functional Genome Annotation

• Prokka

MultiAMR Resistance Gene Annotation

• hAMRonization : Unified ARG Results Report from...
  1) CARD using RGI
  2) AMRFinderPlus
  3) ResFinder

• MultiQC

(back to top)

As there is currently no paper associated with BALROG-ISO, please cite this Github page. Also, I feel free to contact me (edwardbirdlab@gmail.com | edwardbird@ksu.edu) to let me know!

Many tools are used in this pipeline and its respective options. See 'CITATION.md' for the list of all tools used in this pipeline.

(back to top)

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

(back to top)

Edward Bird - - edwardbirdlab@gmail.com | edwardbird@ksu.edu

(back to top)