Data Files and Formats

2.	Data Files and Formats

2.1 Directory Naming Conventions

2.2 Format Requirements for Input FASTA and FASTQ Files

2.3 Standard File Formats

Section 1.3 lists all the files and folders that constitute the deliverable output of the 454 Sequencing System data processing and data analysis software for a generic sequencing Run, including the results of the GS De Novo Assembler and GS Reference Mapper applications. The actual directories generated may contain a number of additional files, but those are intermediate or log files generated for use only by Roche Customer Support personnel, in the event that a Run might require additional investigation.

The 454 Sequencing System software uses fixed names for the files it generates, and the structure and names of the directories allows to differentiate individual sequencing Runs or post-Run analyses. This section describes the nomenclature conventions and file formats used by the software. Examples of the various file types are given in the Sections of this manual that describe each application in detail.

Note that the content of this Section does not apply to the GS Amplicon Variant Analyzer software, whose output structure is completely distinct (beyond the basic data processing files and folders).