- Overview
HGPP( Human Genome haplotype-resolved Program Package ) provides a pipeline for building haplotype resolved human genome by fosmid sequencing
Contributors: Shujia Huang, Yuhui Sun, Xin Tong and Peng Sun
Last Version: 2014-06-18
This package contains: src, extensions, example and img directories
For src: source code for HGPP
For img: Pipeline plot figure
For extensions: Some basic programs for ASE and ASM analysis
For example: Provide some examples for the main processes of HGPP
- Install the software
This package is quit easy to install in your directory,
firstly, you can download this package by :
$ git clone git@github.com:ShujiaHuang/HGPP.git ./
then go into the package directory HGPP and use:
$ make
Then all the required programs will all be compiled and installed automatically. You can find the main part executable programs in bin and find the programs for ASE/ASM analysis in extensions, respectively
- How to use HGPP
You should prepare all the alignment files(BAM/SAM format) before you get start to run this pipeline.
The processes in HGPP:
- Find the fosmid region
- Markers error correction
- Fosmid initial connection
- RefHap phasing process
- haplotype genome reconstruction
- ASE and ASM
We have provided some cases for how we use HGPP in our project in directory example. You could find the detail tutorial information of HGPP in it.
- Please cite the paper
De novo assembly of a haplotype-resolved human genome. Nat. Biotechnol. (2015). doi:10.1038/nbt.3200