Rbowtie2

Rbowtie2 wraps Bowtie2 and AdapterRemoval within R to perform sequencing read alignment, adapter trimming, and paired-end read merging for preprocessing high-throughput sequencing data for downstream genomic analyses.

Key Features:

• Sequencing Read Alignment: Acts as an R wrapper around Bowtie2 to execute alignment of sequencing reads to reference genomes using Bowtie2's alignment algorithms.
• Adapter Trimming and Identification: Integrates AdapterRemoval to detect and trim adapter sequences from raw sequencing reads.
• Read Merging: Supports merging of paired-end reads into single contiguous sequences when appropriate.

Scientific Applications:

• ATAC-seq Analysis: Provides the alignment and adapter-trimming preprocessing steps required for chromatin accessibility profiling in ATAC-seq experiments.
• Genome-wide Studies: Enables high-fidelity read alignment and adapter-free datasets suitable for a range of genome-wide sequencing studies.

Methodology:

Integration of Bowtie2's alignment algorithms with AdapterRemoval's trimming and read-merging processes, executed within an R environment.