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+# ECTyper (an easy typer)
+**ECTyper** wraps a standalone serotyping module.  
+Supports _fasta_ and _fastq_ file formats
+
+# Dependencies:
+- python 3.6.3.*
+- pandas 0.21.0.*
+- samtools 1.5.*
+- bowtie2 2.3.0.*
+- mash 1.1.*
+- bcftools 1.6.*
+- biopython 1.69.*
+- blast 2.2.31 .*
+- seqtk 1.2.*
+
+# Installation
+1. Get `miniconda` if you do not already have `miniconda` or `anaconda`:
+    1. `wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh`
+    1. `bash miniconda.sh -b -p $HOME/miniconda`
+    1. `export PATH="$HOME/miniconda/bin:$PATH"`
+2. Install ectyper  
+    * Directly via `conda`  
+    	1. `conda install -c anaconda -c bioconda -c ubcsamsung ectyper`  
+    * Through `github`  
+    	1. Install dependencies
+          `conda install pandas samtools bowtie2 mash bcftools biopython nose blast seqtk tqdm python=3.6`
+    	1. Download git repository then unzip
+          `wget https://github.com/phac-nml/ecoli_serotyping/archive/master.zip`
+    	1. Install ectyper inside unzipped directory
+          `python setup.py install`
+
+# Basic Usage
+1. Put all of your fasta/fastq files in one folder (concatenate paired files if you want the result to be considered a single entity)
+1. `ectyper -i [file path]`
+1. View the results on the console or in `output/[datatime]/output.csv`
+
+# Example Usage
+* `ectyper -i ecoliA.fasta`  for a single file
+* `ectyper -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna`	for multiple files  
+* `ectyper -i ecoli_folder`	for a folder
+
+# Advanced Usage
+```
+usage: ectyper [-h] -i INPUT [-d PERCENTIDENTITY] [-l PERCENTLENGTH]
+               [--verify] [-s] [-v] [-o OUTPUT]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUT, --input INPUT
+                        Location of new file(s). Can be a single file or a
+                        directory
+  -d PERCENTIDENTITY, --percentIdentity PERCENTIDENTITY
+                        Percentage of identity wanted to use against the
+                        database. From 0 to 100, default is 90%.
+  -l PERCENTLENGTH, --percentLength PERCENTLENGTH
+                        Percentage of length wanted to use against the
+                        database. From 0 to 100, default is 50%.
+  --verify              Enable E. Coli. verification
+  -s, --species         Enable species identification when non-ecoli genome is
+                        found Note: refseq downloading is required when
+                        running this option for the first time.
+  -v, --verbose         Enable detailed output
+  -o OUTPUT, --output OUTPUT
+                        Directory location of output files.
+```
+* The first time species identification is enabled you will need to wait for **ectyper** to download the reference sequence.