String manipulations, efficient matching, and alignments using Biostrings

An introduction to the Biostrings/BSgenome framework (pdf)
Biostrings/BSgenome Lab (pdf)
Biostrings/BSgenome Lab (R script with solutions)
Sequence Alignment of Short Read Data using Biostrings (pdf)
Sequence Alignment of Short Read Data using Biostrings (R script)
topReads.rda (R data file)
Fred Hutchinson Cancer Research Center