AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
Συγγραφέας
Skoufos G., Almodaresi F., Zakeri M., Paulson J.N., Patro R., Hatzigeorgiou A.G., Vlachos I.S.Ημερομηνία
2022Γλώσσα
en
Λέξη-κλειδί
Επιτομή
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. © 2022, The Author(s).