aTRAM

aTRAM assembles targeted gene loci from paired-end Illumina reads using an iterative, reference-guided BLAST and targeted de novo assembly strategy to recover genes for phylogenomic and comparative genomic analyses.

Key Features:

• Targeted De Novo Assembly: Performs targeted de novo assembly of specific loci from a single library of paired-end Illumina reads.
• Iterative Reference-guided Retrieval: Uses an iterative approach integrating a reference sequence and BLAST to identify and recruit reads for assembly.
• Rapid Recovery Across Divergent Taxa: Recovers genes from taxa diverged approximately 25 to 110 million years with reported gene recovery rates of 97%–99%.
• Comparative Efficiency: Assembles sequences in under one minute per gene for closely related taxa while matching the accuracy of reference-based and de novo approaches.
• Reduced Computational Time: Reduces overall assembly time by focusing on loci of interest, enabling locus assemblies to complete in minutes depending on target size.

Scientific Applications:

• Phylogenomics: Enables assembly of orthologous genes across taxa to support phylogenetic inference and study of evolutionary relationships.
• Evolutionary Biology: Supports analyses of genetic divergence and evolutionary history across distantly related taxa.
• Comparative Genomics: Facilitates comparative analyses of gene sequences without requiring comprehensive draft genome assemblies.

Methodology:

Iteratively uses BLAST with a reference sequence to identify and recruit reads from a single library of paired-end Illumina reads and performs targeted de novo assembly of each locus.