##### I have installed mamba so, further steps are-
#### Create a new environment:
mamba create -n ntjoin_env
##### Activate the environment:
conda activate ntjoin_env
##### Install ntJoin:
mamba install -c bioconda -c conda-forge ntjoin=1.1.3

##### Run ntJoin:
target assembly file (my_scaffolds.fa) and a reference assembly file (assembly_ref1.fa),
###### let's scaffold the target assembly:

ntJoin assemble target=my_scaffolds.fa target_weight=1 references='assembly_ref1.fa' reference_weights='2' k=32 w=500
###### This command scaffolds the target assembly using the reference assembly, setting the target assembly weight to 1 and the reference assembly weight to 2. It uses a k-mer size of 32 and a window size of 500.