ATAC

ATAC performs comparative mapping between genome assemblies to validate and improve scaffold order, orientation, and gap filling using whole-genome shotgun assembly data.

Key Features:

• Whole-Genome Shotgun Assembly: Leverages WGSA methodologies exemplified by the Celera human genome assembly (2001) and uses millions of sequencing reads for comparative mapping.
• Paired-end insert strategy: Organizes reads into pairs derived from end-sequencing inserts ranging from 2-kbp to 50-kbp to support scaffold linking and placement.
• Coverage and Quality: Uses quality-trimmed reads covering the genome approximately 5.3× and paired-insert reads covering approximately 39× to increase assembly reliability.
• Comparative Mapping Accuracy: Demonstrates 97% agreement in order and orientation with reference builds such as NCBI Build 34, indicating capability to identify scaffold placement issues.
• Gap Filling: Detects and contributes to filling gaps present in existing genome assemblies such as NCBI Build 34.

Scientific Applications:

• Genome Assembly Validation: Compares newly assembled genomes with reference builds to validate assembly quality and accuracy.
• Genomic Variation and Comparative Genomics: Enables analyses of genetic variation, evolutionary comparisons, and comparative genomics through accurate inter-genome mapping.
• Genome Database Refinement: Improves public genome assemblies by correcting scaffold order and orientation and by filling gaps in builds like NCBI Build 34.

Methodology:

Whole-genome shotgun assembly using millions of reads, organization of reads into paired end-sequencing inserts of 2-kbp to 50-kbp, quality trimming of reads, and comparative mapping against reference assemblies such as NCBI Build 34 to assess order, orientation, and scaffold placement.