SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures.

To install this package with mamba run:

mamba create -n SqueezeMeta -c conda-forge -c bioconda -c fpusan squeezemeta-dev --no-channel-priority --override-channels

And activate it with:

conda activate SqueezeMeta

Detailed usage instructions can be found at http://github.com/jtamames/SqueezeMeta