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1 # ECTyper (an easy typer)
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2 **ECTyper** wraps a standalone serotyping module.
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3 Supports _fasta_ and _fastq_ file formats
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4
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5 # Dependencies:
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6 - python 3.6.3.*
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7 - pandas 0.21.0.*
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8 - samtools 1.5.*
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9 - bowtie2 2.3.0.*
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10 - mash 1.1.*
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11 - bcftools 1.6.*
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12 - biopython 1.69.*
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13 - blast 2.2.31 .*
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14 - seqtk 1.2.*
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15
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16 # Installation
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17 1. Get `miniconda` if you do not already have `miniconda` or `anaconda`:
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18 1. `wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh`
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19 1. `bash miniconda.sh -b -p $HOME/miniconda`
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20 1. `export PATH="$HOME/miniconda/bin:$PATH"`
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21 2. Install ectyper
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22 * Directly via `conda`
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23 1. `conda install -c anaconda -c bioconda -c ubcsamsung ectyper`
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24 * Through `github`
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25 1. Install dependencies
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26 `conda install pandas samtools bowtie2 mash bcftools biopython nose blast seqtk tqdm python=3.6`
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27 1. Download git repository then unzip
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28 `wget https://github.com/phac-nml/ecoli_serotyping/archive/master.zip`
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29 1. Install ectyper inside unzipped directory
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30 `python setup.py install`
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31
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32 # Basic Usage
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33 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)
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34 1. `ectyper -i [file path]`
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35 1. View the results on the console or in `output/[datatime]/output.csv`
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36
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37 # Example Usage
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38 * `ectyper -i ecoliA.fasta` for a single file
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39 * `ectyper -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna` for multiple files
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40 * `ectyper -i ecoli_folder` for a folder
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41
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42 # Advanced Usage
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43 ```
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44 usage: ectyper [-h] -i INPUT [-d PERCENTIDENTITY] [-l PERCENTLENGTH]
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45 [--verify] [-s] [-v] [-o OUTPUT]
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46
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47 optional arguments:
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48 -h, --help show this help message and exit
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49 -i INPUT, --input INPUT
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50 Location of new file(s). Can be a single file or a
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51 directory
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52 -d PERCENTIDENTITY, --percentIdentity PERCENTIDENTITY
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53 Percentage of identity wanted to use against the
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54 database. From 0 to 100, default is 90%.
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55 -l PERCENTLENGTH, --percentLength PERCENTLENGTH
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56 Percentage of length wanted to use against the
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57 database. From 0 to 100, default is 50%.
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58 --verify Enable E. Coli. verification
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59 -s, --species Enable species identification when non-ecoli genome is
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60 found Note: refseq downloading is required when
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61 running this option for the first time.
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62 -v, --verbose Enable detailed output
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63 -o OUTPUT, --output OUTPUT
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64 Directory location of output files.
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65 ```
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66 * The first time species identification is enabled you will need to wait for **ectyper** to download the reference sequence.
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