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diff --git a/README.markdown b/README.markdown index 951892f..d23799e 100644 --- a/README.markdown +++ b/README.markdown @@ -1,7 +1,32 @@ # Quikr # +This is the homepage for quikr. -To install, type "make" in top directory with Makefile. +## What is Quikr ## +Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that +utilizes sparsity promoting ideas from the field of compressed sensing to +reconstruct the composition of a bacterial community (when the input data is +454-like pyrosequencing data). This extremely fast method comes with a default +training database but can be custom trained. Typically reconstruction is +accurate down to the genus level. -See more help and documentation in the doc directory. -http://sourceforge.net/p/quikr/wiki/Home/ +## How Do I Install Quikr ## +Please read the directions on the [installation page](install.markdown). + +## How Do I use Quikr ## +We have several ways to use quikr. Quikr is first and formost a command +line utility, but we also provide python and matlab scripts. + ++ [Command Line Utilities](cli.markdown) ++ [Matlab documentation](matlab.markdown) ++ [Python documentation](python.markdown) + +## Contact ## +For issues with the quikr software, contact gailro@gmail.com + +## Contributors ## ++ David Koslicki ++ Simon Foucart ++ Gail Rosen ++ Calvin Morrison ++ Jean-Luc Bouchot diff --git a/doc/README.markdown b/doc/README.markdown deleted file mode 100644 index d23799e..0000000 --- a/doc/README.markdown +++ /dev/null @@ -1,32 +0,0 @@ -# Quikr # -This is the homepage for quikr. - -## What is Quikr ## -Quikr is a QUadratic, Iterative, K-mer based Reconstruction technique that -utilizes sparsity promoting ideas from the field of compressed sensing to -reconstruct the composition of a bacterial community (when the input data is -454-like pyrosequencing data). This extremely fast method comes with a default -training database but can be custom trained. Typically reconstruction is -accurate down to the genus level. - - -## How Do I Install Quikr ## -Please read the directions on the [installation page](install.markdown). - -## How Do I use Quikr ## -We have several ways to use quikr. Quikr is first and formost a command -line utility, but we also provide python and matlab scripts. - -+ [Command Line Utilities](cli.markdown) -+ [Matlab documentation](matlab.markdown) -+ [Python documentation](python.markdown) - -## Contact ## -For issues with the quikr software, contact gailro@gmail.com - -## Contributors ## -+ David Koslicki -+ Simon Foucart -+ Gail Rosen -+ Calvin Morrison -+ Jean-Luc Bouchot |