iGenomes - BenLangmead/jhu-compute GitHub Wiki
Illumina iGenomes is a distribution of some convenient packages of reference genomes, indexes, and gene annotations. Using these packages can save you time trying to gather these yourself, and might save you from a mistake when the files fail to match up.
I have several iGenomes packages already downloaded and unpacked here:
/scratch0/langmead-fs1/shared/igenomes
get.sh
contains the script I used to get them:
$ cat get.sh
#!/bin/sh
IGENOMES_URL=ftp://igenome:[email protected]
for i in Drosophila_melanogaster/UCSC/dm3/Drosophila_melanogaster_UCSC_dm3.tar.gz \
Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz \
Mus_musculus/UCSC/mm10/Mus_musculus_UCSC_mm10.tar.gz \
Caenorhabditis_elegans/UCSC/ce10/Caenorhabditis_elegans_UCSC_ce10.tar.gz \
Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Escherichia_coli_K_12_MG1655_NCBI_2001-10-15.tar.gz \
Escherichia_coli_K_12_DH10B/NCBI/2008-03-17/Escherichia_coli_K_12_DH10B_NCBI_2008-03-17.tar.gz \
Saccharomyces_cerevisiae/UCSC/sacCer3/Saccharomyces_cerevisiae_UCSC_sacCer3.tar.gz \
Zea_mays/Ensembl/AGPv2/Zea_mays_Ensembl_AGPv2.tar.gz
do
if [ ! -d `dirname $i` ] ; then
wget $IGENOMES_URL/$i
tar zxvf `basename $i`
fi
done