iGenomes

Overview

iGenomes is a collection of reference sequences and annotation files for commonly analyzed organisms. The files were originally generated by Illumina. The files have been downloaded from Ensembl, NCBI, or UCSC, and chromosome names have been changed to be simple and consistent with their download source. On the CCB servers these files can be found at:

/databank/igenomes/

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:

/databank/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf