Processing of shotgun metagenome data

Question

[kocharovskayaj]

Hello, I have a whole metagenome shotgun data processed by trimmomatic, metaspades and bowtie. Please tell me what to do next? It is necessary to find out what organisms are in the samples, as well as to search for genes. Thank you for your answer.

Answer 1

[Carambakaracho]

some suggestions you could go with

• Classification with Kraken2
• Annotation with Prodigal
• Binning using metabat2 (or concoct)
• Assess completeness with BUSCO.

Then you could head down the rabbit hole of functional annotation transfer to figure out what your microbiome is capable of (the MicrobeAnnotator published in Jan 2021 looks promising).