From 7d1e6bff575447d5570e7937dba90bd87f5d79a9 Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Thu, 25 May 2017 12:48:41 +0800 Subject: [PATCH] Update README.md --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 2513dd6..d574da3 100644 --- a/README.md +++ b/README.md @@ -23,9 +23,6 @@ The report of AfterQC is a single HTML page with figures contained in. See an ex * latest: `git clone https://github.com/OpenGene/AfterQC.git` or download [https://github.com/OpenGene/AfterQC/archive/master.zip](https://github.com/OpenGene/AfterQC/archive/master.zip) * stable: [Releases](https://github.com/OpenGene/AfterQC/releases) -# Cite AfterQC -Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics 2017 18(Suppl 3):80 - # Dependency: `AfterQC` uses `editdistance` module for performance. 1, if you are using `standard python`, you can install it using `pip`: @@ -37,11 +34,11 @@ pip install editdistance cd /path/to/AfterQC make ``` -3, Python3 is not supported yet, please use Python2. +3, Python3 is not supported yet, please use Python2. -*** Using `pypy` is suggested, since it's about 3X fast as `standard python`. *** +***Using `pypy` is suggested, since it's about 3X fast as `standard python`.*** -*** If you don't install or build `editdistance` module, `AfterQC` will use a python implementation of editdistance, which will be extremely slow. *** +***If you don't install or build `editdistance` module, `AfterQC` will use a python implementation of editdistance, which will be extremely slow.*** # Simple usage: * Prepare your fastq files in a folder @@ -187,3 +184,6 @@ If you want to eliminate bubble artifact, turn debubble option on (this is slow, * For single-end sequencing data, it will still have `R1`. * `prefilter` means `before filtering`, `postfilter` means `after filtering` * For pair-end sequencing data, `After` will do an `overlap analysis`. read1 and read2 will be overlapped when `read1_length + read2_length > DNA_template_length`. + +# Cite AfterQC +Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics 2017 18(Suppl 3):80