Isas

Isas aligns short-read sequencing data in both color-space and nucleotide-space to enable accurate mapping for CNVseq and RNAseq quantification.

Key Features:

• Dual-space alignment: Supports both color-space and nucleotide-space alignments for short-read sequencing data.
• Uniqueome integration: Leverages the 'uniqueome' to determine the uniquely mappable proportion of genomic sequences at specified error thresholds.
• Pre-computed uniqueome datasets: Provides pre-computed uniqueome data for humans, mice, flies, and worms.
• Fast alignment mechanism: Implements a fast aligning mechanism that uses uniqueome information to improve alignment speed and accuracy.

Scientific Applications:

• RNAseq analysis: Enables accurate mapping of RNAseq reads to support reliable gene expression quantification.
• CNV detection (CNVseq): Provides precise alignments to support detection and analysis of copy number variations.

Methodology:

Performs fast alignment using pre-computed uniqueome data to account for uniquely mappable genomic regions and reduce mapping errors.