For an overview of the design principles and use of Bioconductor sequence classes, see Lawrence et al., 2013, Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): doi:10.1371/journal.pcbi.1003118

For an overview of select high-throughput sequence packages in Bioconductor, see Intermediate Sequence Analysis 2013 section 3.3.

Ranges

IRanges & GenomicRanges

Classes

Methods

Users

Strings and sequences

Biostrings

Users

Data containers

GenomicRanges

VariantAnnotation

ShortRead – FASTQ files

I/O

Approximate data class hierarchy

Annotated
   o metadata
-- Vector
   o many methods (showMethods(class="Vector", where=search()))
   -- Rle
   -- List
      -- SimpleList
         -- DataFrame
         -- Simple*List, e.g., SimpleNumericList
      -- CompressedList (IRanges package)
         -- Compressed*List, e.g., CompressedNumericList
         -- Ranges
            -- IRanges
      -- ... *StringSet, e.g., DNAStringSet
   -- GenomicRanges
      -- GRanges (GenomicRanges package)
   -- ... *String, e.g., DNAString (Biostrings package)
      o transcribe, reverseComplement, pairwiseAligment
SummarizedExperiment (GenomicRanges package)
-- VCF (VariantAnnotation package; readVcf)
ShortReadQ