Is carve me avaiable for de novo assembled contigs from metagenomic data?

[coralzhang]

Hi, I just discovered this tool and find it very interesting. I have whole genome metagenomic sequences from plant roots. I have assembled them into contigs. I used softwares like prokka/prodigal to do gene prediction. Can I use these genes (obviously from many many different bacterial mixed up together) for carveme and get the predicted pathways along with the abundance for those pathways?

[cdanielmachado]

Hi @coralzhang,

CarveMe is designed to transform a genome into a metabolic model. It expects a fasta file as input (preferably with AA sequences). So, if you can generate a fasta file (.faa) with all the proteins predicted by prokka/prodigal, you can give it to CarveMe to build a metabolic model.

However, you have to be careful with the interpretation of this model. Since you are providing metagenomics data with mixed species, the result will be a metabolic network with reactions from mixed species.

If you want to build one metabolic model per species, there are two options:

• Try to build complete metagenome assembled genomes (MAGs) from your metagenomics data. And then build one model for each MAG.

• Try to do taxonomic identification of your species and, if available, download the respective genomes from RefSeq.

If you try any of these options, let me know how it goes.