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comparison ecoli_serotyping/README.md @ 0:7c687720c9e9 draft

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author jpetteng
date Fri, 05 Jan 2018 09:17:33 -0500
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1 # ECTyper (an easy typer)
2 **ECTyper** wraps a standalone serotyping module.
3 Supports _fasta_ and _fastq_ file formats
4
5 # Dependencies:
6 - python 3.6.3.*
7 - pandas 0.21.0.*
8 - samtools 1.5.*
9 - bowtie2 2.3.0.*
10 - mash 1.1.*
11 - bcftools 1.6.*
12 - biopython 1.69.*
13 - blast 2.2.31 .*
14 - seqtk 1.2.*
15
16 # Installation
17 1. Get `miniconda` if you do not already have `miniconda` or `anaconda`:
18 1. `wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh`
19 1. `bash miniconda.sh -b -p $HOME/miniconda`
20 1. `export PATH="$HOME/miniconda/bin:$PATH"`
21 2. Install ectyper
22 * Directly via `conda`
23 1. `conda install -c anaconda -c bioconda -c ubcsamsung ectyper`
24 * Through `github`
25 1. Install dependencies
26 `conda install pandas samtools bowtie2 mash bcftools biopython nose blast seqtk tqdm python=3.6`
27 1. Download git repository then unzip
28 `wget https://github.com/phac-nml/ecoli_serotyping/archive/master.zip`
29 1. Install ectyper inside unzipped directory
30 `python setup.py install`
31
32 # Basic Usage
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)
34 1. `ectyper -i [file path]`
35 1. View the results on the console or in `output/[datatime]/output.csv`
36
37 # Example Usage
38 * `ectyper -i ecoliA.fasta` for a single file
39 * `ectyper -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna` for multiple files
40 * `ectyper -i ecoli_folder` for a folder
41
42 # Advanced Usage
43 ```
44 usage: ectyper [-h] -i INPUT [-d PERCENTIDENTITY] [-l PERCENTLENGTH]
45 [--verify] [-s] [-v] [-o OUTPUT]
46
47 optional arguments:
48 -h, --help show this help message and exit
49 -i INPUT, --input INPUT
50 Location of new file(s). Can be a single file or a
51 directory
52 -d PERCENTIDENTITY, --percentIdentity PERCENTIDENTITY
53 Percentage of identity wanted to use against the
54 database. From 0 to 100, default is 90%.
55 -l PERCENTLENGTH, --percentLength PERCENTLENGTH
56 Percentage of length wanted to use against the
57 database. From 0 to 100, default is 50%.
58 --verify Enable E. Coli. verification
59 -s, --species Enable species identification when non-ecoli genome is
60 found Note: refseq downloading is required when
61 running this option for the first time.
62 -v, --verbose Enable detailed output
63 -o OUTPUT, --output OUTPUT
64 Directory location of output files.
65 ```
66 * The first time species identification is enabled you will need to wait for **ectyper** to download the reference sequence.