Pipeline Features

To do

Features

  • Fast computation of associations between SNP datasets and user-provided trait measurements
  • Parallelised trait analysis
  • Choice of SNP databases for genomic markers

Matapax is fully functional, but here are a couple of features we will implement in the near future:

  • Complete documentation on tool usage
  • Indicate how much longer a job will be kept on the server before deletion.
  • Include input parameters in results
  • Sortable and filterable results tables
  • Gene annotation can be searched to restrict/filter the results table
  • Traits can be visually inspected to see if they fit a normal distribution
  • Traits that do not fit a normal distribution can be transformed
  • Polymorphism information available in result table
  • Kernel density estimated distributions and histograms to visualise trait measurements
  • Box plots of traits and alleles to show segregation of traits and markers
  • Q-Q plots of calculated -log10(p) values
  • Automatic email upon completion
  • Minor allele frequency threshold choice
  • Links to annotation
  • Results can be viewed in a genome browser ( AnnoJ )
  • The ability to calculate/provide P and K matrices for population structure control
  • Crosses between genotypes can be indicated in the traits file by specifying both genotypes separated by a ' x '
  • Replace EMMA with EMMAx
  • Session tracking and a user management system to keep track of your data and jobs
  • Trait management system that allows traits to be renamed as well as transformed and visualised.
  • Publication friendly result data management
  • The ability to query trait response to different polymophisms and alleles under different conditions
  • GO term overrepresentation analysis
  • The ability to show population structure on geographical map and measure of clustering
  • Include in documentation discussion on significance
  • Figure showing coloured markers on chromosome as an overview of the results
  • Provide option for user to restrict SNPs to certain chromosome and region
  • Enable user to test population structure for different combination of accessions for experimental design
  • Efficient SNP storage for faster retrieval
  • The ability to download all data and scripts used in a published job to aid reproducibility
  • The calculation of Best Linear Unbiased Prediction (BLUP)