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