QuickBinDM

Quick binning and frame-shift correction of long read metagenomic assemblies using DIAMOND+MEGAN pipeline with dynamically created reference DB

Overview

QuickBinDM is a bioinformatics pipeline designed to efficiently perform metagenomic binning of contigs generated from nanopore sequencing. The pipeline integrates DIAMOND, MEGAN, and Skani to create a dynamic DIAMOND database, which significantly speeds up the binning process.

Installation

Clone the repository to your local machine:

git clone https://github.com/lucast122/QuickBinDM.git

Requirements

• Python 3.x
• DIAMOND
• MEGAN
• Skani

Please make sure to install the dependencies before running the pipeline.

Usage

Navigate to the directory containing quickbindm.py and execute the following command:

python quickbindm.py -i <input_contigs> -r <reference_seqs> -o <output_folder> [options]

Parameters

Mandatory Parameters

• -i, --input_contigs: The path to the input contigs after assembly and possibly assembly correction. Should be a FASTA or FASTQ file.
• -r, --reference_seqs: The path to the reference sequences for creating the database. Should be a FASTA or FASTQ file.
• -o, --output_folder: The path to the output folder that will contain the results.

Optional Parameters

• -t, --threads: The number of threads to use. Default is 1.
• -a, --ani: The ANI (Average Nucleotide Identity) cutoff. Default is 95.
• -q, --querycoverage: The minimum query coverage for ANI calculation. Default is 80.
• -c, --refcoverage: The minimum reference coverage for ANI calculation. Default is 80.

Example

python quickbindm.py -i input_contigs.fasta -r reference_seqs.fasta -o output/ -t 4 -a 95 -q 80 -c 80

Contributors

• (timo-niklas.lucas@uni-tuebingen.de)