RESEARCH ARTICLE Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons Kemal Eren1, Steven Weaver2, Robert Ketteringham3, Morne Valentyn3, Melissa Laird 4,5 6 6 2 SmithID , Venkatesh Kumar , Sanjay Mohan , Sergei L. Kosakovsky Pond , 6,7 Ben MurrellID * 1 Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA, 2 Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA, 3 Division of Medical Virology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa, 4 Department of Genetics and a1111111111 Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 5 Icahn Institute of a1111111111 Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 6 Division of a1111111111 Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La a1111111111 Jolla, CA, USA, 7 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, a1111111111 Sweden *
[email protected] OPEN ACCESS Abstract Citation: Eren K, Weaver S, Ketteringham R, Next generation sequencing of viral populations has advanced our understanding of viral Valentyn M, Laird Smith M, Kumar V, et al. (2018) population dynamics, the development of drug resistance, and escape from host immune Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS responses. Many applications require complete gene sequences, which can be impossible Comput Biol 14(12): e1006498. https://doi.org/ to reconstruct from short reads. HIV env, the protein of interest for HIV vaccine studies, is 10.1371/journal.pcbi.1006498 exceptionally challenging for long-read sequencing and analysis due to its length, high sub- Editor: TimotheÂe Poisot, Universite de Montreal, stitution rate, and extensive indel variation.