LANL HIV-DB Next Generation Sequence Archive
An HIV, SIV and anti-HIV/SIV antibody ultradeep sequencing repository
The following are Next-Gen primate lentivirus sequence data-sets that may not be accessible through the NCBI Short Read Archive. The files are FTP-downloadable from the links below.
For the NCBI SRA data sets, see our Next-gen Sequences Interface.
How to Submit
If you have a next-gen sequence set you would like to make available through the LANL database archive, you will need to provide:
- A simple text file that will enable a user to understand your file organization and the data sources and sequence naming conventions that you use
- A simple text file that lists the primers used and how they relate to the samples
- A raw data sff file
- The processed alignments you used for basic analysis in your publication
- Contact information
If only one of #3 or #4 is readily available, we would still welcome the submission.
Our goal is to have a very easy to submit and accessible version of primate lentiviral or HIV/SIV antibody deep sequencing published data,
given an expressed need for such a service at several Next-Gen sequencing workshops.
Please contact Brian Foley (firstname.lastname@example.org) and he will assist you in getting the files uploaded to our FTP site
and listed on this page.
Fischer et al. 2010:
Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing.
PubMed ID: 20808830
Redd et al. 2012:
The Rates of HIV Superinfection and Primary HIV Incidence in a General Population in Rakai, Uganda.
PubMed ID: 22675216
last modified: Tue Jan 22 11:09 2013