Bambus

Bambus scaffolds genome assemblies by ordering and orienting contigs using paired-read information and additional linking data to produce ordered, oriented genome scaffolds.

Key Features:

• Contig ordering and orientation: Orders and orients contigs to construct genome scaffolds.
• Paired-read (mate-pair) support: Employs paired-read and mate-pair information as a foundational element in scaffolding.
• Integration of diverse linking data: Integrates various linking data sources, including sequences from completed genomes, beyond traditional mate-pair data.
• Parameterizable scaffolding: Provides extensive control over scaffolding parameters to adjust algorithmic behavior.
• Low-coverage scaffolding: Supports scaffolding of genomes, including mammalian genomes, at low sequencing coverage.
• Haplotype structure analysis support: Aids analysis of haplotype architecture within genomes by improving contig relationships.

Scientific Applications:

• Genome finishing: Supports completion of genome projects by accurately ordering and orienting contigs for scaffold generation.
• Comparative genomics: Facilitates scaffolding based on reference sequences to enable comparative analyses between species or strains.
• Haplotype analysis: Enables investigation of haplotype architecture and genetic diversity within assembled genomes.
• Low-coverage draft scaffolding: Has been applied to scaffold low-coverage draft genomes, including mammalian examples such as the dog genome.

Methodology:

Bambus employs paired-read/mate-pair information and integrates additional linking data, including sequences from completed genomes, to order and orient contigs during scaffolding.