AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

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 strai...

Full description

Saved in:
Bibliographic Details
Published in:Genome Biology 2022-01, Vol.23 (1), p.39-39, Article 39
Main Authors: Skoufos, Giorgos, Almodaresi, Fatemeh, Zakeri, Mohsen, Paulson, Joseph N, Patro, Rob, Hatzigeorgiou, Artemis G, Vlachos, Ioannis S
Format: Article
Language:English
Subjects:
Algorithms
Computational metagenomics
Computer applications
DNA sequencing
Genomes
Identification of contaminants
Islands
Metagenomics
Method
Microbiome
Quantification of microbial abundances
Taxonomy
Time- and space-efficient indexing/alignment
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02610-4