Fig. 4.

Basic methodology of the metagenome analysis through computational tools. The generated metagenome sequences are prefiltered for the removal of low-quality and redundant sequences using Eu-detect and DeConseq. To increase the analytical efficiency of computational tools, the metagenome assemblies are developed using Phrap or Celera or MEGAHIT assembler. This is followed by the prediction of genes using the MEGAN or Gene Mark or Gene Locator and Interpolated Markov Modeler (GLIMMER) program. Function-based annotation and taxonomic profiling are carried out MetaPhlan or Automatic phylogenomic inference application (AMPHORA) or Metaphyler followed by integration into MG-RAST, Integrated Microbial Genomes and Metagenomes (IMG/M) and Genomic Encyclopedia of Bacteria and Archaea (GEBA) like tools