Figaro

Figaro identifies and trims cloning vector sequences from raw DNA sequencing reads to improve genome assembly quality by inferring vector sequences from short oligonucleotide frequency patterns using Poisson statistics without requiring prior knowledge of the vector sequence, splice sites, or adapter sequences.

Key Features:

• Vector sequence inference: Automatically infers vector sequences by analyzing short oligonucleotide frequency using Poisson statistics.
• No prior-sequence requirement: Detects and trims vector, splice site, and adapter sequences without prior knowledge of their sequences.
• High sensitivity and accuracy: Demonstrated 99.98% accuracy on approximately 1.5 million shotgun reads from Drosophila pseudoobscura.
• Improves genome assembly quality: Accurate trimming substantially enhanced whole-genome assembly outcomes, demonstrated by re-assembling two bacterial genomes from shotgun sequences in the NCBI Trace Archive.
• Pipeline integration: Implemented as a fast, lightweight module suitable for incorporation into large computational pipelines.

Scientific Applications:

• Vector clipping from public repositories: Detects and removes unreported vector sequences from datasets such as the NCBI Trace Archive where clipping metadata is missing or inaccurate.
• Draft genome improvement: Supports validation, refinement, and completion of draft-quality genomes by removing contaminating vector sequences prior to assembly.

Methodology:

Infers vector sequence by analyzing short oligonucleotide frequency with Poisson statistics and trims identified vector regions from shotgun sequencing reads.