In the simplest case, the data analysis software applications can take FASTA files and assemble or map the sequences they contain directly, without any preparation. In this case, it treats all the reads present in the FASTA files as single ended, shotgun reads, and assumes that the sequence has been trimmed for quality and for vector, primer, adapter, linker, etc. sequences (all non-sample sequence). The GS De Novo Assembler or the GS Reference Mapper will use all the sequence data present in the file, and produce or map contigs based on those sequences.