gmapR

gmapR performs sequence alignment of RNA-Seq and DNA-Seq reads to genomic references within the R/Bioconductor environment using GMAP and GSNAP algorithms to support transcriptomics, genomics, and epigenetics analyses.

Key Features:

• Advanced Alignment Algorithms: Implements a greedy match-and-extend algorithm with suffix arrays, segment chaining and diagonalization using genomic hash tables, and nucleotide-level dynamic programming accelerated with SIMD instructions.
• Enhanced Genomic Representation: Uses compressed genomic hash tables, enhanced suffix arrays (ESAs), and SIMD-accelerated comparisons to enable alignment against large genomes, including those exceeding four billion base pairs.
• Functional Enhancements: Standardizes indel positions, handles ambiguous splicing events, clips and merges overlapping paired-end reads, and supports alignments to circular chromosomes and alternate scaffolds.
• Integration with R/Bioconductor: Integrates GMAP and GSNAP functionality into R/Bioconductor workflows via packages such as gmapR and HTSeqGenie and provides per-nucleotide tallying of alignments using bam_tally.

Scientific Applications:

• Transcriptomics: Analyzing RNA-Seq data to study gene expression and regulation.
• Genomics: Mapping DNA-Seq reads to reference genomes for variant discovery and structural variation analysis.
• Epigenetics: Investigating genome modifications that affect gene activity without altering DNA sequence.

Methodology:

Computational methods include greedy match-and-extend with suffix arrays, segment chaining and diagonalization via genomic hash tables, compressed genomic hash tables and enhanced suffix arrays (ESAs), and nucleotide-level dynamic programming accelerated with SIMD instructions.