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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 | Bacteria/Archaea

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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

Genome assembly workflow summary so far

raw reads and meta-data exploration

Genome assembly example in bandage and IGB for Bacteroides fragilis NCTC9343 from NCBI

Short reads only genome assembly workflow and plan

Short reads only assembly quality control of short reads automation

Short reads genomes assembly guide and limitations with repeat regions

fastqc quality report reading

fastp use for read processing and trimming

SPAdes as short reads assembler

SPAdes output files for short reads only assembly

Read spades output files and folders to make sense

CheckM2 for Genome assembly quality check – Installation to use Complete Guide

Task to use QUAST for quality check of genomes by yourself

QUAST for quality evaluation | QUAST Part-1/2

QUAST expert mode run for genome quality evaluation | QUAST Part-2/2

QUAST outputs and reading results

use BUSCO as genome assembly quality check | A-Z

Types of genome assemblies based on quality metrics

Tips to improve genome assembly quality

Genome annotation with Prokka and Bakta

Installation and analysis script is available on github

Hybrid Genome Assembly Guide from Raw Reads (short + Long) | A- Z

Results of Unicycler for Hybrid Genome Assembly

Find plasmids in a genome using plassembler

AMR genes and mobile genetic elements | ABRicate and geNomad

geNomad to find mobile genetic elements inside a genome | A-Z

Whole Genome Sequencing and Genome assembly | Summary

Tips to run script step by step for whole genome assembly

Genome taxonomy and script

Genome Taxonomy and database use GTDB-TK | A-Z guide

Average Nucleotide Identity ANI score and cutoffs for novel species

Reading Materials

Quiz Whole Genome Sequencing and Assembly

CompareM2 for genome assembly comparison | Big Pipeline

21: RNAseq/Transcriptomics | for Prokayotes (Bacteria and Archaea)

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01-RNAseq or Transcriptomics | Introduction and plan

02-RNAseq task for students — Must learn from this task

03-RNAseq sessions and tips for learning

04-Central dogma and Transcriptomics

05-Isolate vs. Community of organisms

06-Cultured vs. Uncultured Organisms

07-What is a genome?

08-Key Aspects of a Genome important for Omics

09-Omics Techniques to learn as a Bioinformatics and Transcriptomics

10-RNAseq steps, history and tools | RNAseq vs. Riboseq

11-Task for Single Cell Transcriptomics | What do you think?

12-Types and Methods of Transcriptomics Analysis

13-Bulk RNAseq example in detail

14-Steps involved in RNAseq experiments

15-Study Design in RNAseq experiment Step-1

16-Library preparation and sequencing Step-2

17-Deeper sequencing or More replicates for RNAseq experiment

18-Read length for sequencing for illumna

19-Single End vs. Paired End Reads from Illumina

20-Two important costs for RNAseq Experiments

21-Sequencing short reads but which Illumna sequencing should we go for

22-Learning short reads and long reads sequencing Illumina NanoPore PacBio

23-Data output of sequencing machines | What happens after sequencing?

24-Understand FASTQ file and Quality Score (phred score)

25-FASTA file format vs. FASTQ

26-Important file formats in OMICS | Genomics and other OMICS

27-RNAseq workflow for Bioinformatics

28-RNAseq pipelines for Transcriptomics analysis

29-READemption RNAseq pipeline installation step by step guide

30-Complete RNAseq Analysis A-to-Z Project for Salmonella sp.

31-Task for RNAseq analysis for Students

32-Handling errors for installations and run for READemption

33-Methods to prevent errors for READemption

34-READemption scripts are online on github

35-Read count & Normalization for RNAseq

36-RPKM FPKM TPM and Log2FoldChange in RNAseq

37-READemption Output and results of RNAseq for interpretation

38-DESeq output files reading and understanding

39-Save your data first and then work on it

40-READemption use for future analysis

41-RNAseq analysis on a publication data for Archaea

42-Complete RNAseq run for a Published dataset with Reademption | Started the Analysis

43-Task for Students

44-Pipeline successfully worked for the analysis

45-Paper Output to read and link with Paper Outputs of RNAseq analysis

46-IGB to read coverage files for each RNAseq outputs

47-Docker with DockerHub for any bioinformatics tool

48-Docker uninstallation issue and bugs

49-Google Antigravity for Bioinformaticians and RNAseq + Docker

50-Install Docker for Bioinformatics Tools

51-Use docker for RNAseq analysis with READemption

52-Five step guide for Docker containers use for RNAseq analysis

53-RNAseq analysis for Paired-end reads with three conditions

54-RNAseq analysis for this project and paper with samples and paired-end reads

55-genome fasta and gff files for the sample Organisms

56-Download raw reads for the sample paper for paired end reads

57-Method No. 1 for RNAseq analysis for Paired-end reads

58-Method No. 1 for paired-end reads with analysis example

59-Method No. 2 for RNAseq analysis for Paired-end reads

60-Method No. 2 for RNAseq analysis for Paired-end reads

61-RNAseq analysis results for Merged reads Method No. 2

62-Method No. 3 for RNAseq analysis for Paired-end reads

63-rRNAs are bad for RNAseq analysis, really?

64-Publication ready plots for RNAseq analysis outputs from READemption

65-Task for Students for RNA analysis from a Paper

66-RNAseq visualization Application for READemption output

67-Functional Enrichment Analysis Application is ready

68-Application deployment on streamlit cloud

69-RNAseq course completed

22a: Pangenomics

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01-Introduction to Pangenomics

02 -Tools and Pipelines for Pangenomics analysis for prokaryotes

03 -Task for Pangenomcis run Panaroo analysis

04-Pangenomics Workflow and the importance of generating pangenomes

05-Core vs. Accessory Pangenomes

06 -Pangenomics key concepts

07-PanExplorer for Pangenome Analysis

08-PanExplorer results and report reading for manuscripts

09-Panaroo Pipeline run for Pangenome Analysis (Part-1)

10-Panaroo Pipeline run for Pangenome Analysis (Part-2)

11-Panaroo Results and understanding of outputs

12-Cytoscape for network visualization of pangenome

13-Task to run Anvio workflow for Pangenome analysis

14-Data Visualization for Panaroo Outputs with automatic script and github repo for scripts

22b: Anvio for Pangenomics

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01-Installation of Anvio Pipeline | Anvio for Pangenomics

02-Steps to perform Pangenome analysis using ANVIO pipeline

03-Hands on Pangenome Analysis using Anvio with Real Genomes (Part-1/2)

04-Hands on Pangenome Analysis using Anvio with Real Genomes (Part-2/2)

05 -Task for students to do Pangenome analysis

06-Graphical User Interface of ANVIO Pangenome Main Menu

07-Anvio pangenome BINs and Options

08-Dendograms and layes in Anvio pangenome

09-Search function of Anvio and layers in Anvio Pangenome

10-Legends in Anvio Pangenome

11-Anvio ANI using pyANI and layers on Pangenome

12 -Split pangenome parts from main pangenome

13-Task for Students Anvio Pangenome (Part-1)

14-Task for Students Anvio Pangenome (Part-2)

15-Ideas for Pangenome analysis

16-Important key ideas for Pangenome manuscripts

Bioinformatics Ka Chilla

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