Scaffolder

Scaffolder facilitates construction and reproducible genome scaffolds from fragmented assemblies produced by next-generation short-read sequencing technologies by using YAML (YAML Ain't Markup Language) to specify scaffold structure.

Key Features:

• YAML-based scaffold definition: Defines genome builds as editable plain-text YAML files that specify scaffold structure.
• Gap specification and filling: Allows explicit specification of unknown regions and incorporation of additional sequences to fill known gaps.
• Scaffold assembly operations: Supports joining neighboring sequence regions and filling gaps to produce contiguous scaffold representations from fragmented data.
• Traceability: Records origin information for each scaffold region to maintain provenance within the assembled genome.
• Reproducible plain-text builds: Enables reproducible genome construction by encoding scaffold definitions in plain text rather than editing large FASTA nucleotide sequences.
• Implementation: Implemented in Ruby.

Scientific Applications:

• Genome scaffolding from short-read data: Construction of genome scaffolds for assemblies derived from next-generation short-read sequencing technologies.
• Draft assembly curation: Manual editing and curation of draft genome assemblies to join contigs and resolve gaps.
• Gap closure with known sequences: Incorporation of additional sequence fragments to close or annotate gaps in assemblies.
• Reproducible assembly records: Recording scaffold definitions to support reproducibility and continuity in genome projects.

Methodology:

Scaffolds are defined in YAML plain-text files; the method supports specifying unknown regions, incorporating additional sequences to fill known gaps, and joining neighboring sequence regions; the software is implemented in Ruby.