SGI Altix UV progress report

admin — Thu, 16 Dec 2010 15:43:27 +0000

After a semester of working with the computer, I am extremely happy with it. Really the astonishing thing about the machine is that there is no difference between it, and the desktop PC I’m using to write this post on. The same code that I write, or execute here will work on the machine. I get amazing performance in Bowtie, BWA and other threaded alignment tools.

SGI Altix UV 100

Download Whole Genomes Quickly from NCBI

admin — Wed, 30 Jun 2010 22:04:10 +0000

Here is a quick command line script that should work on any linux system with wget. This command will download chromosomes 1- 8 for the possum. You would need to modify the list of numbers to be “X Y M Un” to get the non-numeric chromosomes.

for i in 01 02 03 04 05 06 07 08; do wget "ftp://ftp.ncbi.nih.gov/genomes/Monodelphis_domestica/CHR_${i}/mdm_ref_chr${i}.fa.gz"; done;

You can do this for any species or really any organized FTP site. Here is the link to the NCBI genome ftp site.

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SGI Altix UV progress report

Download Whole Genomes Quickly from NCBI