In an effort to make NGS data analysis more accessible, Illumina have provided packages of pre-indexed genomes and annotation files in one bundle. For instance you can get the Bowtie/TopHat indexes here for a range of organisms.
The iGenomes are a collection of sequence and annotation files for commonlyRead here for more info.
analyzed genomes. Each iGenome contains data for one species, downloaded from one source (UCSC, NCBI, or Ensembl), for one genomic build.