The Flux Simulator supports quality error models to simulate sequencing errors. The current version of the Flux Simulator comes models, one for reads of length 76 and one for read length 36. The models can also be used for shorter reads.
Applying the error model consists of two steps. First, a quality value is assigned to each position in the read. Second, a cross-talk table is used to check if the base with the given quality
Additionally, error models may be provided. Currently only position-specific errors are supported, see the original discussion on that topic. In short, positional error models base on the simple idea that "problems" that are observed in a certain region of the generated sequence cluster accross multiple reads of the output as they have been influenced by a common temporal and spatial problem during sequencing. Such errors can be estimated empirically after aligning the sequences of a run to the genomic reference sequence and identifying mismatching positions. Especially suited for obtaining such estimations are alignment programs that are not affected by strict limitations on the number of mismatch and hence allow for more complete pictures. The FLUX SIMULATOR provides an automatic error model estimation for alignments output by the GEM aligner. Error models are stored in form of ERR files.
Overview
Content Tools