CAR

CAR orders and orients contigs of prokaryotic draft genomes against a reference genome to produce scaffolds that improve assembly accuracy for downstream comparative and functional genomic analyses.

Key Features:

• Reference-Based Scaffolding: CAR utilizes a closely related organism's reference genome to scaffold contigs, leveraging evolutionary conservation to predict correct order and orientation and addressing challenges from next-generation sequencing technologies that produce draft genomes with numerous independent contigs of unknown relative positions and orientations.
• Input Formats: Accepts contig sets in multi-FASTA format and reference genomes in FASTA format.
• Output Generation: Produces a list of scaffolds composed of ordered and oriented contigs for downstream genomic analyses.

Scientific Applications:

• Microbial genomics: Enables more accurate draft genome assemblies to support analyses of genetic functions, evolutionary relationships, and pathogenic mechanisms.
• Comparative genomics: Facilitates reference-aligned genome comparisons by providing ordered contig scaffolds aligned to a reference.
• Functional annotation: Improves genomic context for annotation of genes and other genomic features.
• Genomic rearrangement analysis: Supports identification and study of genomic rearrangements by ordering contigs relative to a reference genome.

Methodology:

Aligning contigs to a reference genome to infer their correct order and orientation, with optimizations for sensitivity, precision, and genome coverage.