Metagenomic binnig step

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

binnig tools metagenomics

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updated 1.5 years ago by Mensur Dlakic

• written 1.5 years ago by m90 •

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 ?

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written 1.5 years ago by Pierre Lindenbaum

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

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written 1.5 years ago by m90 •

1 answer

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.

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written 1.5 years ago by Mensur Dlakic

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