Home Installation Input and Mapping Parameters and Help Additional Info.

Parameters for different tasks can be set within the program through pop up boxes that are accessible via the "Parameter" menu. In this section all the available parameters will be summarized along with the other menu options available within the software.

• Project: Used to create and delete projects. A project must be created before datasets can be added to it. If a project is deleted all associated datasets will also be deleted.
  1. Add Project: To add a project, a project title is required as well as a template in fasta format. Once a file containing the template is selected any dataset added to the project will be mapped to this template. A variation on this is available under the "Miscellaneous" option.
  2. Delete Project: A project for deletion can be selected. All associated datasets will also be deleted.


• Data: Once a project has been set up, datasets in FASTQ format can be added to it. During this process reads within the dataset will be mapped and aligned to the template associated with the project. The mapping and alignment process is described in more detail in the "Input and Mapping" section of this website.
  1. Add Dataset: A dataset title is required. In addition to this, the project to add the dataset to must be selected. The dataset itseef must be in FASTQ format.
  2. Delete Dataset: Once a project from the dropdown list is selected, a list of datasets associated with that project is displayed. Any of these can be selected for deletion from that project.


• Parameters: The 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).


• Tools: This menu contains some tools to aid in processing next generation data. Additional tools will be added over time.
  1. Sort Bar codes: Reads tagged with a particular bar code can be extracted from a fastq file using this menu option. The user selects the fastq file containing the read data, inputs the bar code to identify the reads of interest and selects the location to save the extracted reads too. The extracted reads will be saved (minus the barcode) in fasta format. If a file contains multiple different bar codes the process should be repeated with each code that the user requires data for i.e. the reads will be binned according to the barcodes.


• About: Version of software v0.0.2.