https://github.com/fpopic/bioinf
(Class) Student assignment project (Bioinformatics)
https://github.com/fpopic/bioinf
bioinformatics debruijn genome
Last synced: 3 months ago
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(Class) Student assignment project (Bioinformatics)
- Host: GitHub
- URL: https://github.com/fpopic/bioinf
- Owner: fpopic
- License: mit
- Created: 2016-12-13T09:39:19.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2017-01-27T16:12:12.000Z (over 8 years ago)
- Last Synced: 2025-01-10T19:42:28.857Z (4 months ago)
- Topics: bioinformatics, debruijn, genome
- Language: C++
- Homepage:
- Size: 21.9 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Student assignment project (Bioinformatics)
**A representation of a compressed de Bruijn graph for pan-genome analysis that enables search**
Goal: Implementation of A1 & A2 algorithms and comparison to the original implementation
Original Paper: https://almob.biomedcentral.com/articles/10.1186/s13015-016-0083-7
Original Implementation: https://www.uni-ulm.de/in/theo/research/seqana.html
Course website: http://www.fer.unizg.hr/predmet/bio
## Dependencies (Project C++ libraries)
Installation will install files in folders:
```
cmake => '/usr'
headers => '/usr/local/include'
sources => '/usr/local/lib'
```
### Install cmake-3.7.1
```sh
cd REPO_FOLDER/install/
unzip cmake-3.7.1.zip
cd cmake-3.7.1
sudo ./bootstrap --prefix=/usr
make
sudo make install
```
### Install sais-2.4.1
```sh
cd REPO_FOLDER/install/
unzip sais-2.4.1.zip
cd sais-2.4.1/
mkdir build
cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="/usr/local"
make
sudo make install
```
### Install sdsl-lite-2.0
```sh
cd REPO_FOLDER/install/
unzip sdsl-lite.zip
cd sdsl-lite/
sudo ./install.sh /usr/local
```
##### Ignore:
```
WARNING: .git/hooks directory does not exists.
The pre-commit hook is not installed.
```
### Google Test 1.8.0
Compiles together with sources as cmake subproject (/test/lib/gtest-1.8.0). No actions needed.
#
### Folder structure after the installation went successful:
```
$ ls usr/local/include/
divsufsort64.h divsufsort.h sais.h sais.hxx sdsl
$ ls /usr/local/lib/
libdivsufsort64.a libsais.a libdivsufsort.a libsdsl.a pkgconfig
```
# Compiling
```
cd REPO_FOLDER/bioinf
cmake --build cmake-build-debug --target debruijn.exe -- -j 4
cd test
cmake --build cmake-build-debug --target debruijn_tests.exe -- -j 4
```
# Running
```
cd REPO_FOLDER/bioinf
mkdir test/res/output
./debruijn.exe test/res/input/XXX.fasta test/res/input/XXX.k test/res/output/XXX.
```
# Running tests
```
cd REPO_FOLDER/bioinf/test
```
All tests
```
./debruijn_tests.exe
```
A1 tests
```
./debruijn_tests.exe --gtest_filter=a1*
```
A2 tests
```
./debruijn_tests.exe --gtest_filter=a2*
```