Rbowtie

Rbowtie provides an R interface to the Bowtie short-read aligner and SpliceMap to align sequencing reads to reference genomes and discover de novo splice junctions for transcriptome and variant analyses.

Key Features:

• Bowtie integration: Leverages the Bowtie short-read aligner to perform rapid mapping of sequencing reads against large reference genomes.
• SpliceMap integration: Utilizes SpliceMap for de novo splice junction discovery and alignment of spliced reads.
• RNA-seq support: Supports alignment and splice-aware analysis of RNA-seq short reads for transcript-level investigations.
• R/Bioconductor interface: Exposes Bowtie and SpliceMap functionality within R and the Bioconductor framework for programmatic workflow integration.
• Interoperability: Enables interoperability with other Bioconductor packages to facilitate downstream analyses such as differential expression and variant processing.

Scientific Applications:

• Transcriptome Analysis: Aligns RNA-seq reads and identifies splice junctions to aid transcript annotation and quantification.
• Variant Calling: Provides alignments of short reads to reference genomes that can be used as input for variant discovery workflows.
• Alternative Splicing Studies: Detects de novo splice junctions to support analyses of alternative splicing events and isoform diversity.

Methodology:

Rbowtie invokes Bowtie for efficient short-read alignment and uses SpliceMap for identification of novel splice junctions.