TAG

TAG assembles metatranscriptomes by leveraging de Bruijn graphs built from matched metagenomic assemblies to improve recovery of transcripts from complex microbial communities.

Key Features:

• Reference-Based Assembly: Uses de Bruijn graphs constructed from matched metagenomic datasets as references to guide metatranscriptome assembly.
• Reads Mapping Algorithm: Maps short metatranscriptomic reads onto the de Bruijn graph using a hash table of junction k-mers that span branching structures.
• Enhanced Transcript Assembly: Overcomes fragmentation in metagenome assemblies to recover more complete and longer transcripts from metatranscriptomic data.
• Implementation and Performance: Implemented in C++ and extensively tested on Linux for performance and reliability.

Scientific Applications:

• Functional profiling of microbial communities: Integrates metatranscriptomic and matched metagenomic datasets to infer functional activity within microbial communities.
• Expression and regulatory analysis: Enables recovery of transcripts missing or truncated in fragmented metagenomes to support analysis of regulatory and expression dynamics.

Methodology:

Constructs a de Bruijn graph from metagenome assemblies and maps metatranscriptomic short reads onto the graph using a hash table of junction k-mers to navigate branching structures and assemble transcripts.