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Add pypy in README
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sfchen committed Jul 28, 2016
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Expand Up @@ -19,14 +19,19 @@ Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 50
* stable: [0.5.0 (released on 2016-07-22)](https://github.com/OpenGene/AfterQC/archive/Release-0.5.0.zip)

# Dependency:
`AfterQC` uses `editdistance` module for performance, if you are using pure `python`, install it using `pip`:
`AfterQC` uses `editdistance` module for performance, if you are using native `python`, install it using `pip`:
```shell
pip install editdistance
```
If you failed to install `editdistance` with `pip`, you can run `make` in the `AfterQC` module to build a `editdistance` library locally with `g++`, and `AfterQC` will load it automatically.

***WARNING: If you don't install or build `editdistance` module, `AfterQC` will use a python implementation of editdistance, but it will be extremely slow.***

# pypy support
* Can be `3X` faster than native `python`
* Run `make` in `AfterQC` folder to build `editdistance` because it is not easy to install it from `pypy pip`
* All figures will not be generated with `pypy`, because `matplotlib` and `PIL` are not supported by `pypy`

# Simple usage:
* Prepare your fastq files in a folder
* For single-end sequencing, the filenames in the folder should be `*R1*`, otherwise you should specify `--read1_flag`
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