IMOS

IMOS aligns noisy long reads to reference genomes to provide accurate and scalable alignments of long-read sequencing data for downstream genomic analyses.

Key Features:

• High Performance on Distributed Systems: Operates on single nodes and distributed clusters to reduce processing time for large genomic datasets.
• Improved Accuracy and Speed: Implements an enhanced version of the Meta-aligner (IM) that achieves up to six times faster performance than the predecessor while maintaining alignment accuracy.
• Scalability with Apache Spark Integration: Leverages Apache Spark to enable deployment and scaling across compute clusters.
• Competitive Multi-node Performance: In multi-node configurations outperforms SparkBWA and reports execution 1.5 times faster than IM and 25 times faster than Minimap2.
• Multi-platform Compatibility: Runs on Linux, Windows, and macOS.

Scientific Applications:

• Genome assembly: Provides rapid alignments of noisy long reads to support assembly of complex genomes.
• Variant calling: Supplies accurate read alignments for detection of single-nucleotide variants and small indels.
• Structural variation analysis: Enables mapping of long reads to identify large insertions, deletions, inversions, and translocations.
• Population genomics: Facilitates large-scale alignment of long-read datasets for comparative and population-level studies.
• Personalized medicine: Supports high-throughput alignment of long-read data for clinical genomics applications.

Methodology:

Enhances the Meta-aligner (IM) for single-node acceleration and integrates Minimap2 with Apache Spark to perform distributed alignment of noisy long-read sequencing data.