DEMO.md

GraphBin-Tk Demo

Setup GraphBin-Tk

First, let's download GraphBin-Tk. Make sure you have git installed.

git clone https://github.com/metagentools/gbintk.git

Now move in to the 'gbintk' directory.

cd gbintk

Let's create an environment for gbintk using the provided environment.yml file. Make sure you have `conda`` installed.

conda env create -f environment.yml

Activate the environment.

conda activate gbintk

Test your installation.

gbintk --help

Now we are all set for the demo.

Test data

Test data for the demo can be found in the tests/data/Sim-5G+metaSPAdes/ folder. Let's set the testing directory path to a variable as shown below so we don't have to type the path every time.

TESTDIR=tests/data/Sim-5G+metaSPAdes/

Run MetaCoAG

Run the following command to bin the test dataset using MetaCoAG.

gbintk metacoag --assembler spades --graph $TESTDIR/assembly_graph_with_scaffolds.gfa --contigs $TESTDIR/contigs.fasta --paths $TESTDIR/contigs.paths --abundance $TESTDIR/coverm_mean_coverage.tsv --output $TESTDIR

Run GraphBin

Run the following command to refine the binning results using GraphBin.

gbintk graphbin --assembler spades --graph $TESTDIR/assembly_graph_with_scaffolds.gfa --contigs $TESTDIR/contigs.fasta --paths $TESTDIR/contigs.paths --binned $TESTDIR/contig_to_bin.tsv --output $TESTDIR

Visualise binning results

Run the following command to visualise the original binning result and the refined binning results on the assembly graph.

gbintk visualise --assembler spades --initial $TESTDIR/contig_to_bin.tsv --final $TESTDIR/graphbin_output.csv --graph $TESTDIR/assembly_graph_with_scaffolds.gfa --paths $TESTDIR/contigs.paths --output $TESTDIR --width 2500 --height 2500

Below are some example visualisations generated.

Initial binning result

Refined binning result