Course Content
00: Resources
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Bioinformatics ka Chilla – LMS Access terms and conditions
01:34
Discord Server
01:49
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
12:27
Bioinformatics Ka Chilla | Complete Registration Process for Bioinformatics Course
01:46
02: Know your Instructor
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Know Your Instructor for Bioinformatics Ka Chilla | Meet the Expert Behind the Bioinformatics Course
10:33
03: What is Bioinformatics?
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Introduction to Bioinformatics for Beginners | Learn Biological Data Science in Urdu | Codanics
12:44
04: Coding for Bioinformatics
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GUI vs CLI for Bioinformatics & Data Science: Which One Should You Choose?
12:40
Tip for Programmers or Coders for Bioinformatics: Automate Tasks and Focus on Scripting
05:26
3 Essential Skills to Become an Expert Bioinformatician | Must-Know Skills for Bioinformatics
09:56
05: Linux-Everything you need to know
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Intro to Linux and Linux Distributions for Bioinformatics and Data Science
11:03
Linux Mint Installation as virtual machine in virtual box in windows
33:01
Linux Mint Installation Guide for Bioinformaticians A – Z in Urdu | Codanics
01:16:56
Keep Your Linux Mint Up to Date with These Easy Commands & Tips | sudo apt update & upgrade
03:57
Screen resolution and font size settings in linux mint
02:28
Startup applications in linux mint can speedup your linux PC
01:14
Install latest codecs and fonts plus extras in linux mint
02:25
Firewall configuration on linux mint for everyone
01:28
Pannel taskbar and folder settings in linux mint
05:07
Keyboard shortcuts to launch panel apps in linux mint
02:06
Night light settings for blue light filter in linux mint using redshift
03:19
TLP package to optimize battery life of linux laptop
01:20
Hot-corners in linux mint for mouse shortcuts
02:42
Mouse / touch pad gestures in linux mint
02:07
Workspaces in linux mint and touchpad gestures
02:07
Desktop zooming options in linux mint for better understanding
03:49
Keyboard Shortcuts for linux mint
02:53
Software manager settings for better results in linux mint
03:12
Install google chrome or any other software for linux mint
02:20
Applets and Desklets in Linux Mint to make your desktop amazingly charming
20:36
Linux Mint Extensions for Desktop Beautification and professional look
09:21
Desktop settings and icons on linux mint
04:03
Basic Linux commands in Linux Mint terminal (Part-1)
17:00
Paths and Working directories in Linux Mint
05:39
Basic Linux Commands in Linux Mint (Part-2)
09:51
File Permission chmod Commands in Linux Mint | Manage File Access Efficiently
09:49
Combining Commands & Using -y Option in Linux Mint | Beginner-Friendly Linux Tips
03:14
Create Your First Shell Script and Execute It in Linux Mint | Beginner Shell Scripting Guide
10:40
Create a Shell Script Using Terminal + wget Command in Linux Mint | Automate File Downloads
10:50
Combine Content of Two Files into One & Write Terminal Output to File in Linux Mint | Easy Guide
05:49
View Large Files Using less, more, head, and tail Commands in Linux Mint Terminal | Easy Tutorial
05:49
grep Commands to View Files with Patterns in Linux Mint and –help Flags for Any Command | Full Guide
15:22
awk BASH Command in Linux Mint for Bioinformatics and Data Science | Data Manipulation Made Easy
24:05
sed BASH Command in Linux for Data Science and Bioinformatics | Text Processing Made Easy
17:33
Terminal Settings in Linux Mint for Bold and Zoomed-In Font Size and Style
07:21
06: Zoom Meetings to know everyone
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Zoom Meeting No. 1
45:50
07: File Formats
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Important File Formats for Linux | CSV, TSV, TXT, FASTQ, FASTQ.GZ, FASTA, fna, faa Explained
55:08
08: VScode installation
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VScode installation and other software installation methods in Linux mint
10:41
09: Conda environments for Bioinformatics
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Conda, Mamba & Python Environments for Bioinformatics and Data Science | Manage Packages Like a Pro
19:49
Install Miniconda in Linux Mint | Step-by-Step Guide for Bioinformatics & Data Science
08:30
Install Mamba in Linux Mint | Faster Alternative to Conda for Bioinformatics & Data Science
03:21
Create Conda Environments in Linux | Comprehensive Miniconda Guide for Bioinformatics & Data Science
32:15
10: git and gitHub
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Git & GitHub in Linux for Bioinformaticians | Version Control Made Easy
10:08
11: R and RStudio
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Install R and RStudio in Linux Using Command Line | Complete Guide for Data Science & Bioinformatics
06:59
R Programming Crash Course (11 h 55 m) – Learn R with Dr Aammar Tufail | Urdu/Hindi #rwithaammar
11:55:37
12: Linux Tool installation and use for Bioinformatics
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Linux tips and updates about software use in bioinformatics
08:01
Tools installation and use | grabseqs and sequences download from NCBI
36:04
Download raw data from a manuscript from NCBI
03:45
Downloading raw data using terminal and other commands
05:18
Download completed in terminal with fasq.gz files having less space
04:54
Metadata related to fastq files and csv file opening in libre office linux
04:19
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
39:23
15: DNA and DNA sequencing
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DNA and DNA Sequencing Technologies | Short Reads vs. Long Reads
33:15
Important Guide about sequencing technology
04:15
Sequencing workflow and fastq files | zipped vs. unzipped files
10:35
Bases vs. Base pairs in genome sequencing
04:44
16: Genes and Genome
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Difference between Genes and Genomes
How big is a genome and how does it looks like?
13:47
17: Prokaryotic vs. Eukaryotic Genomes as bioinformatician’s perspective
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Prokaryotes or unicellular organisms
10:27
Eukaryotes or Multicellular organisms
08:31
Prokaryotes vs. Eukaryotes Major differences
09:19
Prokaryotic genome structure
11:40
How to calculate GC content in a genome?
01:27
Eukaryotic genome structure | Exons vs. Introns
14:07
Genome Size Comparison Prokaryotes vs. Eukaryotic genomes
02:33
Prokaryotic genes vs. Eukaryotic Genes structures
02:54
Why should you start learning from prokaryotic genomes? | Bioinformatics
06:28
Resources and Databases for Prokaryotic & Eukaryotic Bioinformatics
02:17
Tools for Prokaryotic vs. Eukaryotic Bioinformatics analysis
02:21
Real Wold Application and Job Market | Prokaryotic vs. Eukaryotic Bioinformatics
04:25
Complete Guide with Notes
Quizzes-01
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Quizzes for Practice _ Bioinformatics ka chilla
02:12
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
36:46
What is taxonomy?
01:29
Levels of Taxonomy for Bacteria | Understanding Classification Theory with Examples
20:45
18S rRNA and ITS for community analysis | Metabarcoding | Amplicon sequencing
43:19
19: VScode, Git, GitHub, Markdown
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Install and use VScode in Linux as editor and IDE with sync from your github
11:17
VScode experties | files, folders, interface, and settings
10:23
VScode extensions
07:27
Version control systems for coding and git
16:47
Git installation
01:33
Git CheatSheet
Git with terminal | local repository commands
22:55
Git with VScode for local repository making and tracking changes
04:56
hidden folder (.git ) and reseting repo
01:02
Git and GitHub using VScode to sync and use online repo
12:17
Git cloning online public repositories with three methods
05:44
Complete Markdown Guide | 72 Minutes (Adapt to Linux lecture is in Windows)
01:11:23
20: Whole Genome Sequencing (WGS) and Genome Assembly workflow | Bacteria/Archaea
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Intro to whole genome sequencing and assembly
27:24
Select the paper and bacterial strain for raw sequence RAW reads files
36:36
Extract raw reads from NCBI SRA using grabseqs
22:01
Genome assembly workflow summary so far
04:08
raw reads and meta-data exploration
07:56
Genome assembly example in bandage and IGB for Bacteroides fragilis NCTC9343 from NCBI
28:34
Short reads only genome assembly workflow and plan
18:13
Short reads only assembly quality control of short reads automation
30:48
Short reads genomes assembly guide and limitations with repeat regions
26:34
fastqc quality report reading
20:49
fastp use for read processing and trimming
27:07
SPAdes as short reads assembler
13:36
SPAdes output files for short reads only assembly
04:16
Read spades output files and folders to make sense
13:24
CheckM2 for Genome assembly quality check – Installation to use Complete Guide
54:57
Task to use QUAST for quality check of genomes by yourself
00:59
QUAST for quality evaluation | QUAST Part-1/2
07:51
QUAST expert mode run for genome quality evaluation | QUAST Part-2/2
01:52
QUAST outputs and reading results
13:58
use BUSCO as genome assembly quality check | A-Z
22:55
Types of genome assemblies based on quality metrics
11:20
Tips to improve genome assembly quality
08:28
Genome annotation with Prokka and Bakta
30:43
Installation and analysis script is available on github
01:58
Hybrid Genome Assembly Guide from Raw Reads (short + Long) | A- Z
01:14:08
Results of Unicycler for Hybrid Genome Assembly
17:36
Find plasmids in a genome using plassembler
01:31:24
AMR genes and mobile genetic elements | ABRicate and geNomad
13:42
geNomad to find mobile genetic elements inside a genome | A-Z
29:55
Whole Genome Sequencing and Genome assembly | Summary
01:26
Tips to run script step by step for whole genome assembly
06:31
Genome taxonomy and script
01:25
Genome Taxonomy and database use GTDB-TK | A-Z guide
34:17
Average Nucleotide Identity ANI score and cutoffs for novel species
12:00
Reading Materials
Quiz Whole Genome Sequencing and Assembly
02:49
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
22:46
02-RNAseq task for students — Must learn from this task
00:30
03-RNAseq sessions and tips for learning
02:16
04-Central dogma and Transcriptomics
02:11
05-Isolate vs. Community of organisms
02:19
06-Cultured vs. Uncultured Organisms
02:20
07-What is a genome?
01:25
08-Key Aspects of a Genome important for Omics
06:46
09-Omics Techniques to learn as a Bioinformatics and Transcriptomics
08:40
10-RNAseq steps, history and tools | RNAseq vs. Riboseq
12:58
11-Task for Single Cell Transcriptomics | What do you think?
01:15
12-Types and Methods of Transcriptomics Analysis
13:19
13-Bulk RNAseq example in detail
06:08
14-Steps involved in RNAseq experiments
01:56
15-Study Design in RNAseq experiment Step-1
09:58
16-Library preparation and sequencing Step-2
01:18
17-Deeper sequencing or More replicates for RNAseq experiment
17:49
18-Read length for sequencing for illumna
02:48
19-Single End vs. Paired End Reads from Illumina
11:44
20-Two important costs for RNAseq Experiments
02:17
21-Sequencing short reads but which Illumna sequencing should we go for
10:28
22-Learning short reads and long reads sequencing Illumina NanoPore PacBio
01:52
23-Data output of sequencing machines | What happens after sequencing?
02:25
24-Understand FASTQ file and Quality Score (phred score)
06:16
25-FASTA file format vs. FASTQ
01:25
26-Important file formats in OMICS | Genomics and other OMICS
04:46
27-RNAseq workflow for Bioinformatics
06:24
28-RNAseq pipelines for Transcriptomics analysis
11:22
29-READemption RNAseq pipeline installation step by step guide
17:16
30-Complete RNAseq Analysis A-to-Z Project for Salmonella sp.
21:59
31-Task for RNAseq analysis for Students
01:45
32-Handling errors for installations and run for READemption
08:27
33-Methods to prevent errors for READemption
08:35
34-READemption scripts are online on github
03:19
35-Read count & Normalization for RNAseq
16:15
36-RPKM FPKM TPM and Log2FoldChange in RNAseq
14:25
37-READemption Output and results of RNAseq for interpretation
22:57
38-DESeq output files reading and understanding
10:04
39-Save your data first and then work on it
02:15
40-READemption use for future analysis
01:40
41-RNAseq analysis on a publication data for Archaea
07:01
42-Complete RNAseq run for a Published dataset with Reademption | Started the Analysis
23:54
43-Task for Students
01:20
44-Pipeline successfully worked for the analysis
02:12
45-Paper Output to read and link with Paper Outputs of RNAseq analysis
19:20
46-IGB to read coverage files for each RNAseq outputs
15:23
47-Docker with DockerHub for any bioinformatics tool
14:13
48-Docker uninstallation issue and bugs
06:11
49-Google Antigravity for Bioinformaticians and RNAseq + Docker
09:26
50-Install Docker for Bioinformatics Tools
14:21
51-Use docker for RNAseq analysis with READemption
15:59
52-Five step guide for Docker containers use for RNAseq analysis
04:45
53-RNAseq analysis for Paired-end reads with three conditions
04:07
54-RNAseq analysis for this project and paper with samples and paired-end reads
05:35
55-genome fasta and gff files for the sample Organisms
02:58
56-Download raw reads for the sample paper for paired end reads
10:19
57-Method No. 1 for RNAseq analysis for Paired-end reads
09:13
58-Method No. 1 for paired-end reads with analysis example
10:38
59-Method No. 2 for RNAseq analysis for Paired-end reads
03:41
60-Method No. 2 for RNAseq analysis for Paired-end reads
09:30
61-RNAseq analysis results for Merged reads Method No. 2
16:05
62-Method No. 3 for RNAseq analysis for Paired-end reads
03:13
63-rRNAs are bad for RNAseq analysis, really?
10:11
64-Publication ready plots for RNAseq analysis outputs from READemption
19:48
65-Task for Students for RNA analysis from a Paper
01:49
66-RNAseq visualization Application for READemption output
50:28
67-Functional Enrichment Analysis Application is ready
21:57
68-Application deployment on streamlit cloud
04:22
69-RNAseq course completed
01:52
22a: Pangenomics
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01-Introduction to Pangenomics
06:08
02 -Tools and Pipelines for Pangenomics analysis for prokaryotes
09:53
03 -Task for Pangenomcis run Panaroo analysis
03:07
04-Pangenomics Workflow and the importance of generating pangenomes
05:02
05-Core vs. Accessory Pangenomes
22:24
06 -Pangenomics key concepts
08:52
07-PanExplorer for Pangenome Analysis
17:02
08-PanExplorer results and report reading for manuscripts
16:11
09-Panaroo Pipeline run for Pangenome Analysis (Part-1)
25:14
10-Panaroo Pipeline run for Pangenome Analysis (Part-2)
02:21
11-Panaroo Results and understanding of outputs
08:29
12-Cytoscape for network visualization of pangenome
04:19
13-Task to run Anvio workflow for Pangenome analysis
05:44
14-Data Visualization for Panaroo Outputs with automatic script and github repo for scripts
09:09
22b: Anvio for Pangenomics
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01-Installation of Anvio Pipeline | Anvio for Pangenomics
28:40
02-Steps to perform Pangenome analysis using ANVIO pipeline
14:45
03-Hands on Pangenome Analysis using Anvio with Real Genomes (Part-1/2)
33:03
04-Hands on Pangenome Analysis using Anvio with Real Genomes (Part-2/2)
13:57
05 -Task for students to do Pangenome analysis
00:42
06-Graphical User Interface of ANVIO Pangenome Main Menu
20:44
07-Anvio pangenome BINs and Options
16:42
08-Dendograms and layes in Anvio pangenome
03:17
09-Search function of Anvio and layers in Anvio Pangenome
16:19
10-Legends in Anvio Pangenome
02:16
11-Anvio ANI using pyANI and layers on Pangenome
16:04
12 -Split pangenome parts from main pangenome
05:16
13-Task for Students Anvio Pangenome (Part-1)
04:32
14-Task for Students Anvio Pangenome (Part-2)
00:52
15-Ideas for Pangenome analysis
01:48
16-Important key ideas for Pangenome manuscripts
01:38
Bioinformatics Ka Chilla

In this video, I’ll show you how to create a shell script using the Linux Mint terminal and automate file downloading with the powerful wget command. If you want to speed up your workflow, automate repetitive tasks, or learn real-world Linux skills, this tutorial is perfect for you! 🐧⚡ You’ll learn how to write a script that downloads files automatically, making your Linux experience more efficient—especially useful for students, coders, Data Science learners, and Bioinformaticians. ⸻

🔧 What You’ll Learn:

• How to create a new shell script file using nano or touch

• Writing a simple script with the wget command

• How to download files automatically using wget inside a script

• How to make your script executable with chmod +x

• How to run your script from the terminal

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