This new menu allows users access the programs linked to SNPchiMp.
Up to now, we (the SNPchiMp developing team) are the only contributors, but any user is welcome to produce/share their software (freely, and preferibly open-source).
To contribute, please contact: ezequiel [dot] nicolazzie [at] tecnoparco [dot] org.
PEDDA_ROW - This program allows you to convert the Illumina FinalReport file in ROW format into a ped/map (PLINK) file format.
PEDDA_MATRIX - This program allows you to convert the Illumina FinalReport file in MATRIX format into a ped/map (PLINK) file format.
iConvert - The iConvert program allows you to convert genotype allele call formats (any format for any SNP chip contained in the SNPchiMp tool) of PLINK files. This software is open-source and coded in Python.
AffyPipe - The AffyPipe pipeline automatizes the Affymetrix standard and "best practice" genotyping workflows for Linux and Mac users (and allows obtaining edited PLINK files!). This pipeline is open-source and coded in Python.
Third-party software (not necessarily linked to SNPchimp, but useful):
PLATO 2.0 - The Ritchie Lab - Penn State University. PLATO is a PLatform for the Analysis, Translation and Organization of large-scale data in a standalone program.