SqueezeMeta

SqueezeMeta performs automated metagenomic and metatranscriptomic processing from raw reads to genomic bins, enabling co-assembly, read mapping for gene abundance estimation, and genome binning for microbial community analysis, including support for nanopore sequencing data.

Key Features:

• Fully automated workflow: Implements end-to-end metagenomic and metatranscriptomic processing including read processing, co-assembly, gene prediction, binning, and result storage.
• Co-assembly capability: Supports multi-metagenome co-assembly across an unlimited number of samples and performs read mapping to estimate gene abundances per metagenome.
• Binning and bin checking: Recovers individual genomes via binning procedures and applies internal checks to assess contig and bin consistency.
• Database storage: Stores analysis results in a MySQL database for downstream querying and export.
• Analysis-platform integration: Provides custom scripts for integration with anvi'o and an R package to interface SqueezeMeta outputs for downstream analyses and plotting.

Scientific Applications:

• Gut microbiome analysis: Demonstrated on 32 gut metagenomes, recovering several million genes and hundreds of genomic bins.
• Metagenomic and metatranscriptomic surveys: Applicable to community profiling, gene abundance estimation, and genome-resolved metagenomics across diverse microbial environments, including nanopore sequencing datasets.

Methodology:

Computational steps explicitly include read processing, co-assembly, read mapping for gene abundance estimation, gene prediction, genomic binning with contig/bin consistency checks, result storage in a MySQL database, and integration via custom anvi'o scripts and an R package.