BitMapper

BitMapper maps next-generation sequencing (NGS) reads to a reference genome and identifies all possible mapping locations to enable comprehensive analysis of genetic variation, including insertions, deletions (indels), and mismatches.

Key Features:

• All-mapping capability: Identifies all potential mapping locations for each read within a reference genome, including alignments containing insertions, deletions (indels), and mismatches.
• Vectorized bit-vector algorithm: Employs a novel vectorized bit-vector algorithm to calculate edit distances simultaneously between a single read and multiple reference locations.
• Verification optimization: Performs simultaneous edit-distance computations to substantially reduce the time required for verification, the most time-consuming part of mapping.
• Performance efficiency: Experimental evaluations on simulated and real datasets report speed improvements ranging from several-fold up to an order of magnitude versus state-of-the-art all-mappers while achieving higher sensitivity.
• Implementation: Implemented in C.

Scientific Applications:

• Comprehensive variant discovery: Enables detection of genetic variants, including indels and mismatches, by reporting all possible read placements.
• Structural variation and novel-variant identification: Supports identification of structural variations and novel genetic variants that may be missed by best-match mappers.
• Complex disease genomics: Provides exhaustive alignment information useful for studies of complex genetic disorders.
• Evolutionary and population genomics: Facilitates analyses in evolutionary biology and population genomics that require complete mapping information.
• Personalized medicine: Supplies comprehensive mapping data beneficial for workflows in personalized medicine that depend on exhaustive read placement.

Methodology:

Maps reads to a reference genome using a vectorized bit-vector algorithm that performs simultaneous edit-distance calculations between a single read and multiple reference locations to accelerate verification; implemented in C.