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+# 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
+