Aquila_stLFR

Aquila_stLFR identifies structural variants by performing haplotype-resolved assembly of stLFR linked-read sequencing data to detect and characterize deletions and insertions in diploid genomes.

Key Features:

• Haplotype-Based Assembly: Leverages the phasing ability of stLFR linked-reads to partition reads into haplotype-specific blocks and assemble each haplotype for diploid genome reconstruction.
• SV Detection: Detects medium to large deletions (50bp – 10kb) with high sensitivity and insertions with high specificity.
• Genome-wide SV Reconstruction: Reconstructs genome-wide structural variants from the assembled haplotypes.
• Dependencies: Requires Python3 and libraries numpy, pysam, scipy, and uses external tools SAMtools and minimap2.

Scientific Applications:

• Structural variant discovery: Characterizing deletions and insertions in genomic studies using stLFR linked-read data.
• Haplotype-resolved diploid assembly: Producing independent assemblies of each haplotype for comprehensive diploid genome analysis.
• Benchmarking and validation: Performance has been benchmarked on sample NA24385 to demonstrate efficacy in SV detection.

Methodology:

Partitioning of linked reads into two haplotype-specific blocks using stLFR phasing; independent assembly of each haplotype block; reconstruction of genome-wide structural variants from the assembled haplotypes.