MetaGT

MetaGT integrates metagenomic assemblies with de novo metatranscriptome assemblies to improve metatranscriptome contiguity and completeness and to quantify transcript abundances from Illumina sequencing data.

Key Features:

• Integration of metatranscriptomic and metagenomic data: Aligns metatranscriptome assemblies with metagenome assemblies from the same sample to fill missing regions and improve assembly contiguity and completeness.
• De novo metatranscriptome assembly: Performs de novo assembly of metatranscriptomic reads to capture active gene expression profiles in microbial communities.
• Support for Illumina sequencing data: Accepts Illumina-derived metagenome and metatranscriptome sequencing datasets as input.
• Extraction of coding DNA sequences (CDSs): Extracts CDSs that are covered by transcripts to enable downstream functional analyses.
• Estimation of transcript abundances: Quantifies transcript abundances from assembled metatranscriptomic data.
• Implementation in NextFlow: Implemented using NextFlow to define the pipeline workflow and execution.

Scientific Applications:

• Functional activity profiling: Determining active genes and their expression levels in microbiomes to study functional activity under varying conditions.
• Microbial community dynamics: Investigating gene function and microbial community responses to environmental changes through improved metatranscriptome assemblies.

Methodology:

Performs de novo assembly of metatranscriptomic reads, aligns metatranscriptomic contigs to metagenomic assemblies to fill gaps and enhance assembly quality, extracts CDSs covered by transcripts, and estimates transcript abundances; the pipeline is implemented in NextFlow.