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

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

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

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 <A1 or A2> 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*