On the CCB servers these files can be found at:
The Ensembl and UCSC annotation and sequence files for the following organisms are available under these directories:
Human /databank/igenomes/Homo_sapiens/ Mouse /databank/igenomes/Mus_musculus/ Rat /databank/igenomes/Rattus_norvegicus/ Zebrafish /databank/igenomes/Danio_rerio/ Drosophila /databank/igenomes/Drosophila_melanogaster/ Chicken /databank/igenomes/Gallus_gallus/ Pig /databank/igenomes/Sus_scrofa/ Chimpanzee /databank/igenomes/Pan_troglodytes/
In these directories you will find sub-directories for Ensembl and UCSC annotation and sequence for different builds, for example:
/databank/igenomes/Homo_sapiens/UCSC/hg19/Annotation /databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
Indices for Bowtie, Bowtie2 & BWA, and fastq format files of sequence are all in the Sequence directory:
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index /databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex /databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex
Annotation files eg gtf files can be found in the Annotation directory: