Illumina iGenome FTP

Illumina Provided Genomes

Illumina provides a number of commonly used genomes at ftp.illumina.com along with a reference annotation:
• Arabidopsis_thaliana
• Bos_taurus
• Caenorhabditis_elegans
• Canis_familiaris
• Drosophila_melanogaster
• Equus_caballus
• Escherichia_coli_K_12_DH10B
• Escherichia_coli_K_12_MG1655
• Gallus_gallus
• Homo_sapiens
• Mus_musculus
• Mycobacterium_tuberculosis_H37RV
• Pan_troglodytes
• PhiX
• Rattus_norvegicus
• Saccharomyces_cerevisiae
• Sus_scrofa
You can login using the following credentials:
• Username: igenome
• Password: G3nom3s4u
For example, download the FASTA, annotation, and bowtie index files for the human hg18 genome from the iGenomes repository with the following commands:
>wget --ftp-user=igenome --ftp-password=G3nom3s4u ftp://ftp.illumina.com/Homo_sapiens/UCSC/hg18/Homo_sapiens_UCSC_hg18.tar.gz
Unpack the tar file:
tar xvzf Homo_sapiens_UCSC_hg18.tar.gz
Unpacking will make its own folder
Homo_sapiens/UCSC/hg18