HT-ARGfinder

HT-ARGfinder (Horizontally Transferred Antibiotic Resistant Genes finder) a pipeline that detects and enumerates horizontally transferred ARGs in metagenomic data while also estimating the directionality of transfer.

Requirements

1. Conda installed
2. ~350GB space for GTDB-tk (https://ecogenomics.github.io/GTDBTk/installing/index.html)

Installation

git clone https://github.com/Badhan023/HTARGfinder.git
conda create -n htargfinder -c conda-forge -c bioconda gtdbtk=1.3.0
conda activate htargfinder
cd HTARGfinder
./setup.sh

The setup.sh will take ~4 hours for GTDB-tk.

Running HT-ARGfinder

Activate the conda for this tool, i.e., htargfinder in this case, before running the pipeline.

bash pipeline.sh sample sample_read1.fq sample_read2.fq database   #1 paired-end library in fastq format

Here, sample is the desired prefix of the intermediate and output files, sample_read1.fq and sample_read2.fq are the paired-end reads as inputs. database is the ARG database prefix. Currently there are two options for this argument: CARD, and DeepARG.

Outputs

1. sample_HTARGs_database.csv (horizontally transferred ARG-list with donor & recepient information according to the ARG database selected)
2. sample_diamond_out_default_database.csv (ARG matches running DIAMOND against the ARG database selected)
3. sample_taxonomy_DeepARG-DB.csv (taxonomic information of the bins associated with horizontally transferred ARGs according to the ARG database selected)

Database Options User can add another database, for example newdb.fa in this pipeline by simple running the following command.

diamond makedb --in newdb.fa -d reference_newdb

When the database is ready to use, user can simply use newdb as the fourth argument of pipeline.sh as another option for ARG database. For example,

bash pipeline.sh sample sample_read1.fq sample_read2.fq newdb