Dr. Salzberg's interest in the human genome project motivated him to develop one of the first computational gene-finding systems for the human genome in the early 1990s. His initial collaborations with TIGR at that time led to the development of the Glimmer gene finder, which has been used in the analysis of thousands of bacterial, archaeal, and viral genomes, including Borrelia burgdorferi (the Lyme disease bacterium), Treponema pallidum (the syphilis bacterium), Mycobacterium tuberculosis, Vibrio cholerae, Bacillus anthracis(anthrax), and many others. He and his research team developed a eukaryotic gene finder for Plasmodium falciparum, the malaria parasite, and later adapted it for the human genome, the model plant Arabidopsis thaliana, Oryza sativa (rice), Cryptococcus neoformans, Brugia malayi, and other species. Salzberg's lab has a major focus on next-generation sequence alignment and on large-scale genome assembly. They have assembled hundreds of genomes, large and small, and have developed a variety of assembly software systems, including the open-source AMOS assembly package. In recent years they have developed several pioneering, highly efficient systems for alignment of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems, which are now used by thousands of labs around the world. All of the group's software is free and open source, and their systems have been downloaded hundreds of thousands of times. In addition to his software systems, Salzberg has contributed analyses to many genome sequencing projects, including the human genome, multiple plant and animal genomes, and many bacteria. He was a co-founder of the Influenza Genome Sequencing Project, the first large-scale genomics study of human and avian influenza viruses.