2022 Bioinformatics Algorithms

Setup (make sure you have python3.10)

pip install -r requirements.txt

HW1: Python practice

cd hw1
python hw1.py

Input: hw1/HW1.txt Output: hw1/HW1_ans.txt

HW2: Python practice II

Read Clinvar VCF

cd hw2
python hw2.py

Input: hw2/HW2_clinvar.txt Output: hw2/hw2_clnsig.png hw2/hw2_rs.tsv

HW2_2: Bash practice

cd hw2_2
./hw2_2.sh

Input: /localpath/a_very_big_trash.tar.gz Output: hw2_2/answer/home.txt, hw2_2/answer/location.txt

Week3: Blast and read mapping

see week3/README.md

HW3: Read Blast Result

Some pair of sequences are mapped on the reference by blast,

and then calculate the insertion size of the pair.

Some pair should be removed if the mapping result doesn't meet some criteria.

cd hw3
python hw3.py

input: hw3/rat_sample.fa Output: hw3/rat_sample_merge.stat.csv

Week4: Metagenomics

see week4/README.md

HW4: N50 and Metagenomics Result Interpretation

cd hw4
# N50 practice
python hw4_1.py > hw4.1.txt
# Parse Result of https://github.com/metagenome-atlas/Tutorial.git and answer questions
python hw4_2.py > hw4.2.txt

input: HW4.1.txt Tutorial/Example Output: hw4.1.txt HW4.2.txt hw4.2.png

HW5: Read Sam/Bam format

Extract the phased genotype of specific position from sam file.

cd hw5
python hw5.py

input: hw5.sam (Not provided), ITGA2B.vcf Output: hw5.ITGA2B.count.tsv hw5.chr17.*.strange_case.bam

Week5: Graph genome

see week5/README.md

cd week5
python week5_graph.py

input: NA Output: week5/c3.sample.c3_vg.sort.gam.gai week5/c3.sample.c3_hisat.bam

Week6: Protein structure prediction

see week6/README.md

HW6: Protein structure prediction

see hw6/README.md

Final: Final exam (coding)

see final/README.md

linnil1 / 2022_bioinformatics_algorithms