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# Falcon 安装与样例

[TOC levels=1-3]: # " "
- [Falcon 安装与样例](#falcon-安装与样例)
- [RS II 与 Sequel 对比](#rs-ii-与-sequel-对比)
- [文档](#文档)
    - [[几个术语](http://www.pacb.com/wp-content/uploads/2015/09/Pacific-Biosciences-Glossary-of-Terms.pdf)](#几个术语)
    - [[Falcon 参数](https://github.com/PacificBiosciences/FALCON/wiki/Manual)](#falcon-参数)
    - [Falcon 结果文件](#falcon-结果文件)
- [分析平台的历史](#分析平台的历史)
- [安装 GenomicConsensus 和 falcon](#安装-genomicconsensus-和-falcon)
    - [安装Linuxbrew](#安装linuxbrew)
    - [通过 pitchfork 编译](#通过-pitchfork-编译)
    - [直接安装 falcon-integrate, 现在不推荐](#直接安装-falcon-integrate-现在不推荐)
- [falcon 样例数据](#falcon-样例数据)
    - [`falcon/example` 里的 [*E. coli* 样例](https://github.com/PacificBiosciences/FALCON/wiki/Setup:-Complete-example).](#falconexample-里的-e-coli-样例)
    - [Scer S288c](#scer-s288c)

doc/pacbio_consensus.md  view on Meta::CPAN

* [UC DAVIS](http://dnatech.genomecenter.ucdavis.edu/2016/11/10/new-service-long-read-sequencing-on-the-pacbio-sequel/)
* Falcon 问题合集
    * [Trace assembled and unassembled reads in FALCON](https://github.com/PacificBiosciences/FALCON/issues/472)
    * [Is there any need to polish the assembly result with quiver?](https://github.com/PacificBiosciences/FALCON/issues/304)
    * [minimum sequencing depth requirement for FALCON](https://github.com/PacificBiosciences/FALCON/issues/256)
    * [Hybrid Assembly using falcon](https://github.com/PacificBiosciences/FALCON/issues/282)
    * 调整 falcon 参数
        * [Falcon assembly](https://github.com/PacificBiosciences/FALCON/issues/308)
        * [how to set the appropriate config file for larger genome using local mode](https://github.com/PacificBiosciences/FALCON/issues/466)

## [几个术语](http://www.pacb.com/wp-content/uploads/2015/09/Pacific-Biosciences-Glossary-of-Terms.pdf)

* Subreads - 测序仪直接输出的实时序列, SMRTbell 两个接头之间的序列.
* CCS - 对于较短的模板, 聚合酶在会在环形的 SMRTbell 上环绕多次, 即对同一序列测序多次. 得到的保守序列即为 CCS.
* Long reads - 模板较长, 聚合酶没有抵达 SMRTbell 另一端的接头.
* `.subreads.bam` - 可直接用于分析的 subreads.
* `.scraps.bam` - 接头, 标签和可能有问题的 subreads.

## [Falcon 参数](https://github.com/PacificBiosciences/FALCON/wiki/Manual)

* input_fofn - 输入的 fasta 文件路径