+
+
+
+
+ {% if site.google_analytics %}
+
+ {% endif %}
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+++ b/docs/index.md
@@ -1,4 +1,4 @@
-Home
+Contents
====
[![Build Status](https://travis-ci.org/chungongyu/siga.svg?branch=master)](https://travis-ci.org/chungongyu/siga)
@@ -14,7 +14,7 @@ Home
* [Running SIGA](#running-siga)
* [Benchmarks](#benchmarks)
* [Citation](#citation)
-* [Related Publications](#related-publications)
+* [Publications](#publications)
* [FAQ](#faq)
* [Support](#support)
* [Authors](#authors)
@@ -22,7 +22,7 @@ Home
Overview
========
-SIGA is an open-source _de novo_ assembly toolkit containing various assembly pipelines which are totally compatible with [SGA](https://github.com/jts/sga) file format. Similar to [SGA](https://github.com/jts/sga), it is designed as a [modular set of programs](#running-siga), which are used to form an assembly pipeline.
+SIGA is an open-source _de_ novo assembly toolkit containing various assembly pipelines which are totally compatible with [SGA](https://github.com/jts/sga) file format. Similar to [SGA](https://github.com/jts/sga), it is designed as a [modular set of programs](#running-siga), together which form an assembly pipeline.
Quick Start
===========
@@ -37,6 +37,8 @@ Quick Start
* [rapidjson](https://github.com/Tencent/rapidjson)
* [gperftools](https://github.com/gperftools/gperftools) (optional but suggested)
+Dependencies may be installed using the package manager [Homebrew](https://homebrew.sh) on macOS and [Linxubrew](http://linuxbrew.sh) on Linux and Windows, using [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/).
+
### Compiling SIGA
If you cloned the repository from github, run `autogen.sh` from the root directory
@@ -134,30 +136,36 @@ siga index --help
Benchmarks
========
-Comming soon...
+Comming soon ...
Citation
========
## [SIGA](https://github.com/chungongyu/siga)
-Chungong Yu, Yu Lin, Guozheng Wei, Bing Wang, Yanbo Li and Dongbo Bu. **SIGA** : A Sensitive and Intelligent *de* novo Genome Assembler.
+Chungong Yu, Yu Lin, Guozheng Wei, Bing Wang, Yanbo Li and Dongbo Bu. **SIGA** : An open-source Sensitive and Intelligent *de* novo Genome Assembler.
-Related Publications
-====================
+Publications
+============
-None yet! ^_~
+None yet! ^_~
FAQ
====
1. **Where can I get further help or advice?**
- See [Support](#support) or the [siga wiki](https://github.com/chungongyu/siga/wiki).
+ See [Support](#support) or the [siga wiki](https://github.com/chungongyu/siga/wiki).
+
+2. **What parameters should I tune to improve my assembly?**
+
+ See [here](https://github.com/chungongyu/siga/wiki/SIGA-parameter-tuning)
Support
=======
+[Create a new issue](https://github.com/chungongyu/siga/issues) on GitHub.
+
Contact [siga@ict.ac.cn](mailto:siga@ict.ac.cn)
Authors