abacas

abacas aligns, orders, and orients shotgun-assembled contigs to a reference genome using MUMmer alignments to generate contiguated pseudomolecules for genome finishing.

Key Features:

• Alignment and Synteny Identification: ABACAS employs MUMmer's Nucmer and Promer to align contigs against a reference and identify conserved syntenic blocks.
• Pseudomolecule Generation: It processes alignments to order and orient contigs and generate pseudomolecules that account for overlapping contigs and gaps.
• Alignment Filtering: Alignments are refined using MUMmer's delta-filter utility to improve placement accuracy.
• Visualization Integration: ABACAS integrates with the ACT comparative browser to visualize alignment results and synteny relationships.
• Primer Design: The tool automatically designs PCR primer sequences to target and close assembly gaps.
• tblastx Support: tblastx can be used to analyze contigs not incorporated into the pseudomolecule.

Scientific Applications:

• Strain-level genome finishing: Facilitates contiguation of assemblies when sequencing closely related strains to produce high-quality draft genomes.
• Next-generation sequencing assembly improvement: Transforms shotgun assemblies from next-generation sequencing technologies into contiguated genome sequences for downstream analyses.

Methodology:

abacas aligns draft assembly contigs to a reference using MUMmer's Nucmer and Promer, filters alignments with the delta-filter utility, processes those alignments to generate pseudomolecules accounting for overlaps and gaps, uses tblastx for contigs not incorporated into the pseudomolecule, and designs primers to close gaps.