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Christina-hshi committed Apr 11, 2020
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# SH-assembly
SH-assembly is a bioinformatic pipeline for de novo genome assembly.
SH-assembly is a de Bruijn-graph based method.
It is a de Bruijn-graph based method.
It counts the k-mers using CQF-deNoise followed by contracting unbranched paths in DBG graph to unitigs.
The unitig graph then will be simplified using the graph simplification module in [Minia 3](https://github.com/GATB/minia).
In the original Minia 3 program, we can not directly call its simplication module.
Here we provide the modification upon Minia 3 (v3 git commit n3eb6f54), using which we can directly call the simplification module.

## External libraries
- z
- bz2
- boost
- tbb
- **z**
- **bz2**
- **boost**
- **tbb**

## Installation
git clone https://github.com/Christina-hshi/SH-assembly.git
#in project root directory,
#go to project root directory
cd SH-assembly
mkdir release
cd release
cmake ..
#this will make all targets, including a customed version of CQF-deNoise, and assembly program.
make
#this will make all targets, including a customized version of CQF-deNoise, and assembly program.
make
cd ..

#install a customized version of minia, where the simplification module can be run as an idenpendent step.
git clone https://github.com/Christina-hshi/Minia.git
cd Minia
git submodule init
git submodule update
mkdir release
cd release
cmake ..
make -j8

## User mannual
The basic workflow of running SH-assembly is
1. run "CQF-deNoise" to counting kmers
2. run "Contiger" to building unitig graph
3. run "minia" to simplify unitig graph, and produce a list of contigs.

1. run **CQF-deNoise** to counting kmers
2. run **Contiger** to building unitig graph
3. run **Minia** to simplify unitig graph, and produce a list of contigs.

For each program, run the program without arguments for usage instructions.

## Contact
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