GALA

GALA assembles gap-free chromosome-scale genomes from PacBio and Nanopore long-read sequencing data to produce accurate chromosome-level genome assemblies.

Key Features:

• Chromosome-by-Chromosome Assembly: Implements a multi-layer computer graph framework to identify mis-assemblies in preliminary assemblies or chimeric raw reads and partition data into chromosome-scale linkage groups.
• Mis-assembly/Error Reduction: Independently assembles each linkage group to eliminate mis-assembly errors and produce gap-free assemblies.
• Integration of Multiple Data Sources: Incorporates Hi-C data, genetic maps, reference genomes, and motif analyses into the assembly process.
• Cross-platform Long-read Support: Operates on PacBio and Nanopore long reads, with demonstrated performance on PacBio high-fidelity (HiFi) reads.
• De novo Assembly of Diverse Species: Has been applied to de novo assemble genomes such as Caenorhabditis elegans and Arabidopsis thaliana using combined PacBio and Nanopore datasets.
• Human Genome Finishing: Can achieve gap-free human genome assemblies with the aid of a reference genome.

Scientific Applications:

• De novo genome assembly: Produces gap-free chromosome-scale assemblies for model organisms and other species using long-read data.
• Human genome finishing: Enables generation of gap-free human assemblies when a reference genome is available.
• Genomic structural analysis: Supports detailed study of genomic structures and functions across organisms.
• Biomedical research: Facilitates investigations into genetic diseases and applications in personalized medicine.
• Evolutionary biology: Supports comparative and evolutionary studies through high-quality assemblies.

Methodology:

Uses a multi-layer computer graph to detect mis-assemblies and chimeric reads, partitions data into chromosome-scale linkage groups, independently assembles each linkage group, and integrates Hi-C, genetic maps, reference genomes, and motif analyses with PacBio and Nanopore long reads (including PacBio HiFi).