Monthly Archives: June 2010

Download Whole Genomes Quickly from NCBI

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.

Welcome

Welcome to my updated portfolio. Please stay tuned as I add information about my current work, publications and even some code.