Parameter values used within the software can be set under this menu option. Each sub option will result in a popup box containing sliders to adjust the associated values.
  1. K-mer Matching is used to find the approximate location of a read against the template. Briefly, prior to mapping all unique k-mers of length k are identified on the template along with their locations. Subsequently, individual reads are divided into k-mers of equal length and in each case, the k-mers within the read are matched to the template k-mers. A plot of the location frequencies then reveals the approximate location of the read.
    1. k-mer Size: This is the size of the k-mers used during mapping.
    2. Read Density This is the minimum number of k-mer hits a region of the template must have before being considered as being a candidate for read location. After k-mer indexing a window of length equal to that of the read length (+10) is moved along the template. In each window the average per site number of k-mer hits for the read are calculated. The window with the highest number of hits is considered as the most likely location for the read. If no window contains a value higher than the threshold specified by this parameter the read is considered too diverse to be a match.
    3. k-mer Skip: When a read is divided into k-mers these are matched against a template. However if the data has little variation within it, it may not be necessary to look up every single k-mer within the read. This parameter allows the user to choose a step size between k-mers. For example, if the value of 2 is chosen then every second k-mer with the read will be used during mapping instead of every k-mer.
  2. Pairwise Alignment After mapping is complete, reads are automatically pairwise aligned to the location that they are a closest match to.
    1. Match: Character match score.
    2. Gap Open: Score for opening a gap within the alignment.
    3. Gap Extension: Score for extending a gap with the alignment.
    4. Transversion: Score for a transversion.
    5. Transition: Score for a transition.
  3. Miscellaneous
    1. Replace template with con. during mapping: If this parameter is set to true the software will remap reads to a consensus of the origional assembly (see "Input And Mapping" page).
    2. No. Of Threads: This sets the number of treads used in processing. The default value is the (number of cores avaiable - 1).
  4. Predator
    1. HPS+ Error Rate (Mismatch): The error rate, for mismatches occuring inside of homopolymeric stretchs, used by Predator.
    2. HPS- Error Rate (Mismatch): The error rate, for mismatches occuring outside of homopolymeric stretchs, used by Predator.
    3. HPS Run Length: Length of homopolymeric stretches used by Predator.