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AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite.

Giorgos SkoufosFatemeh AlmodaresiMohsen ZakeriJoseph N PaulsonRob PatroArtemis G HatzigeorgiouIoannis S Vlachos
Published in: Genome biology (2022)
We introduce AGAMEMNON ( https://github.com/ivlachos/agamemnon ) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNON delivers accurate abundances at genus, species, and strain resolution. It incorporates a time and space-efficient indexing scheme for fast pattern matching, enabling indexing and analysis of vast datasets with widely available computational resources. Host-specific modules provide exceptional accuracy for microbial abundance quantification from tissue RNA/DNA sequencing, enabling the expansion of experiments lacking metagenomic/metatranscriptomic analyses. AGAMEMNON provides an R-Shiny application, permitting performance of investigations and visualizations from a graphics interface.
Keyphrases
  • microbial community
  • antibiotic resistance genes
  • single cell
  • single molecule
  • high resolution
  • rna seq
  • nucleic acid
  • circulating tumor
  • cell free
  • wastewater treatment
  • circulating tumor cells
  • visible light