Final BSc thesis is a course held at University of Zagreb, Faculty of Electrical Engineering and Computing in the sixth semester of the undergraduate study. The main focus is to apply knowledge and skills obtained from Software Design Project course to recreate or improve existing methods which are widely used in bioinformatics. Under the supervision of prof. Mile Šikić, students will implement one such algorithm, thoroughly test it on simulated and real data, and formally encapsulate the whole process by writing and defending a thesis. Each student will have access to a private branch of this repository, on which this README will be updated with the specific task.
In this thesis, a tool for genome upper bound assembly was created. It was fully written in C++ and tested on couple of datasets. Tool outputs percentage of the genome coverage that is possible to build in an ideal case considering sequenced data provided at the input. It also creats a graph file in GFA format. Algorithms like sweep line, depth-first search and Needleman–Wunsch were implemented. Tool was tested on datasets of Escerichia coli and yeast Saccharomyces cerevisiae. It might be mainly used in evaluating quality of the sequenced data and other de novo assembly methods.
Tool can be installed by running bash script
bash install.shYou can run tool either by passing reads and genome to script
bash run.sh <reference genome> <reads file>or by passing all needed files to tool directly
build/bin/assembly <PAF file> <reference file> <repeats file> <reads file>Reads file need to be in FASTA or FASTQ format, PAF file is generated from Minimap tool and repeats file can be generated either by RED tool or by tool written by Sara Bakić: https://github.com/lbcb-edu/BSc-thesis-18-19/tree/sbakic
Tool can be tested on an Oxford Nanopore Technologies data set obtained by sequencing the Escherichia coli K-12 substr. MG1655 genome. The data set is freely available from Loman Labs here, while the reference genome is freely available from NCBI here.
Laboratory for Bioinformatics and Computational Biology cannot be held responsible for any copyright infringement caused by actions of students contributing to any of its repositories. Any case of copyright infringement will be promptly removed from the affected repositories and reported to appropriate faculty organs.