GitHub repo for this course - Codanics

Course Content

00: Resources

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Bioinformatics ka Chilla – LMS Access terms and conditions

Linux/Unix Cheatsheet

GitHub repo for this course

01: Course Introduction and Registration

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Course Introduction: Bioinformatics Ka Chilla | A Complete Course on Bioinformatics

Bioinformatics Ka Chilla | Complete Registration Process for Bioinformatics Course

02: Know your Instructor

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Know Your Instructor for Bioinformatics Ka Chilla | Meet the Expert Behind the Bioinformatics Course

03: What is Bioinformatics?

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Introduction to Bioinformatics for Beginners | Learn Biological Data Science in Urdu | Codanics

04: Coding for Bioinformatics

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GUI vs CLI for Bioinformatics & Data Science: Which One Should You Choose?

Tip for Programmers or Coders for Bioinformatics: Automate Tasks and Focus on Scripting

3 Essential Skills to Become an Expert Bioinformatician | Must-Know Skills for Bioinformatics

05: Linux-Everything you need to know

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Intro to Linux and Linux Distributions for Bioinformatics and Data Science

Linux Mint Installation as virtual machine in virtual box in windows

Linux Mint Installation Guide for Bioinformaticians A – Z in Urdu | Codanics

Keep Your Linux Mint Up to Date with These Easy Commands & Tips | sudo apt update & upgrade

Screen resolution and font size settings in linux mint

Startup applications in linux mint can speedup your linux PC

Install latest codecs and fonts plus extras in linux mint

Firewall configuration on linux mint for everyone

Pannel taskbar and folder settings in linux mint

Keyboard shortcuts to launch panel apps in linux mint

Night light settings for blue light filter in linux mint using redshift

TLP package to optimize battery life of linux laptop

Hot-corners in linux mint for mouse shortcuts

Mouse / touch pad gestures in linux mint

Workspaces in linux mint and touchpad gestures

Desktop zooming options in linux mint for better understanding

Keyboard Shortcuts for linux mint

Software manager settings for better results in linux mint

Install google chrome or any other software for linux mint

Applets and Desklets in Linux Mint to make your desktop amazingly charming

Linux Mint Extensions for Desktop Beautification and professional look

Desktop settings and icons on linux mint

Basic Linux commands in Linux Mint terminal (Part-1)

Paths and Working directories in Linux Mint

Basic Linux Commands in Linux Mint (Part-2)

File Permission chmod Commands in Linux Mint | Manage File Access Efficiently

Combining Commands & Using -y Option in Linux Mint | Beginner-Friendly Linux Tips

Create Your First Shell Script and Execute It in Linux Mint | Beginner Shell Scripting Guide

Create a Shell Script Using Terminal + wget Command in Linux Mint | Automate File Downloads

Combine Content of Two Files into One & Write Terminal Output to File in Linux Mint | Easy Guide

View Large Files Using less, more, head, and tail Commands in Linux Mint Terminal | Easy Tutorial

grep Commands to View Files with Patterns in Linux Mint and –help Flags for Any Command | Full Guide

awk BASH Command in Linux Mint for Bioinformatics and Data Science | Data Manipulation Made Easy

sed BASH Command in Linux for Data Science and Bioinformatics | Text Processing Made Easy

Terminal Settings in Linux Mint for Bold and Zoomed-In Font Size and Style

06: Zoom Meetings to know everyone

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Zoom Meeting No. 1

07: File Formats

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Important File Formats for Linux | CSV, TSV, TXT, FASTQ, FASTQ.GZ, FASTA, fna, faa Explained

08: VScode installation

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VScode installation and other software installation methods in Linux mint

09: Conda environments for Bioinformatics

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Conda, Mamba & Python Environments for Bioinformatics and Data Science | Manage Packages Like a Pro

Install Miniconda in Linux Mint | Step-by-Step Guide for Bioinformatics & Data Science

Install Mamba in Linux Mint | Faster Alternative to Conda for Bioinformatics & Data Science

Create Conda Environments in Linux | Comprehensive Miniconda Guide for Bioinformatics & Data Science

10: git and gitHub

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Git & GitHub in Linux for Bioinformaticians | Version Control Made Easy

11: R and RStudio

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Install R and RStudio in Linux Using Command Line | Complete Guide for Data Science & Bioinformatics

R Programming Crash Course (11 h 55 m) – Learn R with Dr Aammar Tufail | Urdu/Hindi #rwithaammar

12: Linux Tool installation and use for Bioinformatics

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Linux tips and updates about software use in bioinformatics

Tools installation and use | grabseqs and sequences download from NCBI

Download raw data from a manuscript from NCBI

Downloading raw data using terminal and other commands

Download completed in terminal with fasq.gz files having less space

Metadata related to fastq files and csv file opening in libre office linux

13: Sequencing Technologies

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Seuencing Technologies

14: Quality Control of Short Reads

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Quality control of short reads using fastqc and multiqc | understanding number of threads in Linux

15: DNA and DNA sequencing

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DNA and DNA Sequencing Technologies | Short Reads vs. Long Reads

Important Guide about sequencing technology

Sequencing workflow and fastq files | zipped vs. unzipped files

Bases vs. Base pairs in genome sequencing

16: Genes and Genome

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Difference between Genes and Genomes

How big is a genome and how does it looks like?

17: Prokaryotic vs. Eukaryotic Genomes as bioinformatician’s perspective

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Prokaryotes or unicellular organisms

Eukaryotes or Multicellular organisms

Prokaryotes vs. Eukaryotes Major differences

Prokaryotic genome structure

How to calculate GC content in a genome?

Eukaryotic genome structure | Exons vs. Introns

Genome Size Comparison Prokaryotes vs. Eukaryotic genomes

Prokaryotic genes vs. Eukaryotic Genes structures

Why should you start learning from prokaryotic genomes? | Bioinformatics

Resources and Databases for Prokaryotic & Eukaryotic Bioinformatics

Tools for Prokaryotic vs. Eukaryotic Bioinformatics analysis

Real Wold Application and Job Market | Prokaryotic vs. Eukaryotic Bioinformatics

Complete Guide with Notes

Quizzes-01

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Quizzes for Practice _ Bioinformatics ka chilla

Quiz No. 1: Linux and Conda Quiz

Quiz No. 2: Prokaryotes, Eukaryotes, Genes, Genomes & Sequencing Technologies

18: Marker Gene Analysis | 16S rRNA, 18S rRNA, ITS

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16S rRNA gene and its importance for Microbial Ecology

What is taxonomy?

Levels of Taxonomy for Bacteria | Understanding Classification Theory with Examples

18S rRNA and ITS for community analysis | Metabarcoding | Amplicon sequencing

19: VScode, Git, GitHub, Markdown

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Install and use VScode in Linux as editor and IDE with sync from your github

VScode experties | files, folders, interface, and settings

VScode extensions

Version control systems for coding and git

Git installation

Git with terminal | local repository commands

Git with VScode for local repository making and tracking changes

hidden folder (.git ) and reseting repo

Git and GitHub using VScode to sync and use online repo

Git cloning online public repositories with three methods

Complete Markdown Guide | 72 Minutes (Adapt to Linux lecture is in Windows)

20: Whole Genome Sequencing (WGS) and Genome Assembly workflow

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Intro to whole genome sequencing and assembly

Select the paper and bacterial strain for raw sequence RAW reads files

Extract raw reads from NCBI SRA using grabseqs

Bioinformatics Ka Chilla

Github repo for bioinformatics: https://github.com/AammarTufail/bioinformatics_ka_chilla

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