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diff --git a/doc/cli.markdown b/doc/cli.markdown new file mode 100644 index 0000000..c7f8e11 --- /dev/null +++ b/doc/cli.markdown @@ -0,0 +1,64 @@ +# Quikr Command Line Utilities # + +Quikr has three command-line utilities that mirror the behavior of the python +module and the matlab implementation. The advantage of this is ease of scripting +and job management. These utilities are written in python and wrap the quikr +module. + +## quikr\_train ## + +The quikr\_train is a tool to train a database for use with the quikr tool. +Before running the quikr utility, you need to generate the trained matrix or +download a pretrained matrix from our database\_download.html. + +### Usage ### +quikr\_train returns a custom trained matrix that can be used with the quikr +function. You must supply a kmer. + +quikr\_train's optional arguments: + -i, --input, the database of sequences (fasta format) + -o, --output, the trained matrix (text file) + -k, --kmer, the kmer size (integer) + -z, --compress compress the output matrix with gzip (flag) + +## quikr ## +Quikr returns the estimated frequencies of batcteria present when given a +input FASTA file. A default trained matrix will be used if none is supplied +You must supply a kmer and default lambda if using a custom trained matrix. + +quikr's optional arguments: + -f, --fasta, the fasta file sample + -o, --output OUTPUT, the output path (csv output) + -t, --trained-matrix, the trained matrix + -l, --lamb, the lambda size. (the default lambda value is 10,000) + -k, --kmer, this specifies which kmer to use (default is 6) + + +### Troubleshooting ### + +If you are having trouble, and these solutions don't work. Please contact the +developers with questions and issues. + +#### Broken Pipe Errors #### +Make sure that you have the count-kmers and probablilties-by-read in your +$PATH, and that they are executable. + +If you have not installed quikr system-wide, you'll need to add the folder +location of these binaries in the terminal before running the command: + + PATH = $PATH:/path/to/quikr/src/nbc/ + +Make sure that the binaries are executable by running: + + chmod +x probabilities-by-read + chmod +x count-kmers + +#### Python Cannot Find XYZ #### + +Ensure that you have Python 2.7, Scipy, Numpy, and BIOpython installed +and that python is setup correctly. You should be able to do this from a python +prompt without any errors: + >>> import numpy + >>> import scipy + >>> from Bio import SeqIO + diff --git a/doc/index.markdown b/doc/index.markdown new file mode 100644 index 0000000..5b3c430 --- /dev/null +++ b/doc/index.markdown @@ -0,0 +1,30 @@ +# 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.html). + +## How Do I use Quikr ## +We have several ways to use quikr. There is a python module, command line +scripts, and matlab scripts. + ++ [Matlab documentation](matlab.html) ++ [Python documentation](python.html) ++ [Command Line Utilities](cli.html) + +## Contributors ## ++ David Koslicki ++ Gail Rosen ++ Calvin Morrison ++ Jean-Luc Bouchot + diff --git a/doc/install.markdown b/doc/install.markdown new file mode 100644 index 0000000..cbbbe21 --- /dev/null +++ b/doc/install.markdown @@ -0,0 +1,18 @@ +# How Can I Install The Quikr Utility? # +To use Quikr there are several prerequisites. + +Base Requirements: ++ Mac OS X or GNU/Linux or Unix-based operating system+ ++ Python 2.7, Scipy, Numpy, BIOPython modules ++ 4Gb of RAM minimum. Absolutely neccessary. + +We also have a Quikr implementation in Matlab so that you can easily integrate +Quikr into your custom programs and scripts. + +Our Quikr code is available on our sourceforge download page: + +[http://sourceforge.net/projects/quikr/](sourceforge project page) + +Our development GIT repository is available here: + +[http://rosalind.ece.drexel.edu/git/quikr/](rosalind.ece.drexel.edu/git/quikr/) |