• Specifying the instrument type and the application type:

• Four types of instrument systems produce data that NextGENe can analyze – the Roche/454 instrument series, the Illumina Genome Analyzer, and Life Technologies’s SOLiD System and Ion Torrent sequencer. You must specify the instrument type that you used to produce the data that is being analyzed.

• The application type determines how you are going to analyze the data – de novo Assembly, SNP/Indel Discovery, and so on. The application type that you specify, in turn, determines the steps that are available to you for analyzing your data – Sequence Condensation, Sequence Assembly, and Sequence Alignment. You must also specify the method by which to analyze the data and the number of cores that are to be used for processing the data.

• Loading the data files – The data files that are being analyzed must be in .fasta format or BAM format. With the exception of the BAM format, if the files are not in .fasta format, for example, .fastq, then you must use the NextGENe conversion tool to convert the files before loading them. See To load the sample data files.

• Loading the reference files – For all application types other than de novo Assembly, a reference is required for aligning reads. The reference can be a .fasta file, a GenBank file, a preloaded reference that SoftGenetics supplies, or for STR analysis, a custom .fasta file that you create. See To load the reference files.

• Specifying the output location and saving the output file – You must specify the location for the output folder and the name of the output folder. See To specify the output file name and location.

• Specifying the values for the analysis steps – You can accept the default values that NextGENe generates, or you modify the values as needed. See To specify the values for the data analysis steps.

• Specifying post-processing options for the project – Optionally, you can specify which outputs (reports and sequences) to automatically generate and save after project analysis for a sequence alignment project is completed. See To specify the post-processing options for a Sequence Alignment project.

• Run the project – You can process a single project, or you can process multiple projects sequentially. You can also carry out a secondary analysis on a previously run project. See To finish the project.