The Roche Genome Sequencer FLX and FLX Titanium Systems, the Illumina Genome Analyzer, Life Technologies’s SOLiD System, or the Ion Torrent sequencer generate millions to hundreds of millions of the short sequence reads, and each instrument supplier has its own format or formats for organizing the reads and assigning the quality scores. Before you use NextGENe to analyze this data, you must use the NextGENe Format Conversion tool to convert the supplier’s format to a standard .fasta format that NextGENe can read. Optionally, you can also use the tool to trim or remove low quality reads before analysis.