Introduction

GraphMB is a Metagenomic Binner developed for long-read assemblies, that takes advantage of graph machine learning algorithms and the assembly graph generated during assembly. It has been tested on (meta)flye assemblies.

Installation

Option 1 - From wheel::

pip install https://github.com/AndreLamurias/GraphMB/releases/download/v0.1.2/graphmb-0.1.2-py3-none-any.whl

Option 2 - From source::

git clone https://github.com/AndreLamurias/GraphMB cd GraphMB python -m venv venv; source venv/bin/activate # optional pip install .

Option 3 - From anaconda::

conda install -c andrelamurias graphmb

Option 4 - From pip

pip install graphmb

Input files

The only files required are the contigs in fasta format, and the assembly graph in GFA format. For optimal performance, the assembly graph should be generated with Flye 2.9, since it includes the number of reads mapping to each pair of contigs. Also, for better results, CheckM is run on each contig using the general Bacteria marker sets. This is optional though, you can just run the model for a number of epochs and pick the last model. By default, it runs with with early stopping.

In summary, you need to have a directory with these files:

  • edges.fasta

  • assembly_graph.fasta

  • edges_depth.txt (output of jgi_summarize_bam_contig_depths)

  • marker_gene_stats.csv (optional)

You can get an example of these files https://drive.google.com/drive/folders/1m6uTgTPUghk_q9GxfX1UNEOfn8jnIdt5?usp=sharing Download from this link and extract to data/strong100.