Metagenomic binnig step

Question

[m90]

Hi all,

I'm trying to use Metagenome Binning on the Linux terminal, and I've downloaded MaxBin version 2.2.2. The package exists, but it's not working, and I'm not sure why. When I try to run the command run_MaxBin.pl, I get an error saying that the command is not found.

Could you please help me figure out how to use the MaxBin2 package in a Conda environment on the terminal? Also, how can I run the following command in Bash?

run_MaxBin.pl -thread 8 -contig JC1A_contigs.fasta -reads ../../data/trimmed_fastq/JC1A_R1.trim.fastq.gz -reads2 ../../data/trimmed_fastq/JC1A_R2.trim.fastq.gz -out MAXBIN/JC1A

[Pierre Lindenbaum]

check the PATH . https://opensource.com/article/17/6/set-path-linux

Could you please help me figure out how to use the MaxBin2 package in a Conda environment on the terminal?

it's not clear: do you have installed the tool above with conda ?

[m90]

Yes , I installed with conda a private environment, the package exist but command line not working

Answer 1

[Mensur Dlakic]

There are two MaxBin2 conda packages. I tried the one listed below and it works:

conda install bioconda::maxbin2

There are better binning programs than MaxBin2, such as MetaBAT2 and VAMB. The former is a C-based program and doesn't require a special environment for installation.

• https://bitbucket.org/berkeleylab/metabat/src/master/
• https://github.com/RasmussenLab/vamb