GRAbB

GRAbB assembles specific genomic regions from Next-Generation Sequencing (NGS) data to recover multi-copy and single-copy loci for phylogenetic and epidemiological analyses.

Key Features:

• Targeted Assembly: Assembles selected genomic regions by using a known part of the region such as a PCR amplicon sequence or a homologous sequence from a related species.
• Multi-Region Capability: Targets multiple genomic regions within a single run.
• Homology-Based Extraction: Extracts specific loci based on sequence homology, including sequences used for barcoding.
• Multi-copy and Single-copy Support: Recovers both multi-copy regions and single-copy loci that are often poorly assembled by generic assemblers.
• Efficiency: Reports superior performance compared to MITObim in speed, memory usage, and disk space efficiency.
• Versatility: Enables exhaustive assembly of complex regions such as the rDNA repeat region and mitochondrial genome and extraction of homologous genes including IGS, RPB1, RPB2, and TEF1a.

Scientific Applications:

• Phylogenetic studies: Recovery of targeted loci and multi-copy regions to inform phylogenetic inference.
• Epidemiological research: Assembly of genomic regions relevant to strain identification and outbreak analysis.
• Mitochondrial genome analysis: Exhaustive assembly of mitochondrial genomes from NGS reads.
• rDNA repeat region analysis: Reconstruction of rDNA repeat regions for comparative and evolutionary studies.
• Barcoding and gene recovery: Extraction of homologous barcode loci and genes such as IGS, RPB1, RPB2, and TEF1a for genetic and ecological studies.

Methodology:

Targeted baiting from NGS reads using a known sequence seed (e.g., PCR amplicon or homologous sequence) and homology-based extraction of loci, allowing multiple regions to be targeted in a single run.