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HIV sequence database

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:
  1. 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
  2. A simple text file that lists the primers used and how they relate to the samples
  3. A raw data sff file
  4. The processed alignments you used for basic analysis in your publication
  5. 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 ( and he will assist you in getting the files uploaded to our FTP site and listed on this page.

LANL Archive

Fischer et al. 2010: Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing.
PubMed ID: 20808830

Archer et al. 2012: Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.
PubMed ID: 23166726
PLOS ONE: Article

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

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