Course Computatoional Genomics

Materials for course of Computational genomics on School of Electrical Engineering

Getting Started

Clone the repository and run notebooks in Jupyter environment:

jupyter-notebook &

Python 3 from www.python.org
pip3
python3 -m pip install --upgrade pip
python3 -m pip install jupyter
pip3 install pandas
pip3 install nose

The list of project assignments.

Name		Name	Last commit message	Last commit date
notebooks		notebooks
LICENSE		LICENSE
Lesson_01_Genome_Informatics.pdf		Lesson_01_Genome_Informatics.pdf
Lesson_02_Exact_String_Matching.pdf		Lesson_02_Exact_String_Matching.pdf
Lesson_03_Suffix_Trie_Suffix_Tree_Approximate_Matching.pdf		Lesson_03_Suffix_Trie_Suffix_Tree_Approximate_Matching.pdf
Lesson_04_Burrows_Wheeler_Transform_and_FM_index_Alignment.pdf		Lesson_04_Burrows_Wheeler_Transform_and_FM_index_Alignment.pdf
Lesson_05_Workflows_VC_Cancer.pdf		Lesson_05_Workflows_VC_Cancer.pdf
Lesson_06_Edit_distance_and_dynamic_programming.pdf		Lesson_06_Edit_distance_and_dynamic_programming.pdf
Lesson_06b_Weighted_edit_distance_and_global_alignment.pdf		Lesson_06b_Weighted_edit_distance_and_global_alignment.pdf
Lesson_07_Local_alignment.pdf		Lesson_07_Local_alignment.pdf
Lesson_07b_Bowtie_BLAST.pdf		Lesson_07b_Bowtie_BLAST.pdf
Lesson_08_Genome_Assembly_SCS.pdf		Lesson_08_Genome_Assembly_SCS.pdf
Lesson_08b_OLC_assembly.pdf		Lesson_08b_OLC_assembly.pdf
Lesson_09_DeBruijn_graph_assembly.pdf		Lesson_09_DeBruijn_graph_assembly.pdf
Lesson_09b_Error_correction.pdf		Lesson_09b_Error_correction.pdf
Lesson_09c_Scaffolding.pdf		Lesson_09c_Scaffolding.pdf
README.md		README.md