Linux/Unix Cheatsheet

GitHub repo for this course

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

01: Course Introduction and Registration

Video - 00:12:27 mins

Bioinformatics Ka Chilla | Complete Registration Process for Bioinformatics Course

Video - 00:01:46 mins

02: Know your Instructor

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

Video - 00:10:33 mins

03: What is Bioinformatics?

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

Video - 00:12:44 mins

04: Coding for Bioinformatics

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

Video - 00:12:40 mins

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

Video - 00:05:26 mins

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

Video - 00:09:56 mins

05: Linux-Everything you need to know

Intro to Linux and Linux Distributions for Bioinformatics and Data Science

Video - 00:11:03 mins

Linux Mint Installation as virtual machine in virtual box in windows

Video - 00:33:01 mins

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

Video - 01:16:56 mins

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

Video - 00:03:57 mins

Screen resolution and font size settings in linux mint

Video - 00:02:28 mins

Startup applications in linux mint can speedup your linux PC

Video - 00:01:14 mins

Install latest codecs and fonts plus extras in linux mint

Video - 00:02:25 mins

Firewall configuration on linux mint for everyone

Video - 00:01:28 mins

Pannel taskbar and folder settings in linux mint

Video - 00:05:07 mins

Keyboard shortcuts to launch panel apps in linux mint

Video - 00:02:06 mins

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

Video - 00:03:19 mins

TLP package to optimize battery life of linux laptop

Video - 00:01:20 mins

Hot-corners in linux mint for mouse shortcuts

Video - 00:02:42 mins

Mouse / touch pad gestures in linux mint

Workspaces in linux mint and touchpad gestures

Desktop zooming options in linux mint for better understanding

Video - 00:03:49 mins

Keyboard Shortcuts for linux mint

Video - 00:02:53 mins

Software manager settings for better results in linux mint

Video - 00:03:12 mins

Install google chrome or any other software for linux mint

Video - 00:02:20 mins

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

Video - 00:20:36 mins

Linux Mint Extensions for Desktop Beautification and professional look

Video - 00:09:21 mins

Desktop settings and icons on linux mint

Video - 00:04:03 mins

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

Video - 00:17:00 mins

Paths and Working directories in Linux Mint

Video - 00:05:39 mins

Basic Linux Commands in Linux Mint (Part-2)

Video - 00:09:51 mins

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

Video - 00:09:49 mins

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

Video - 00:03:14 mins

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

Video - 00:10:40 mins

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

Video - 00:10:50 mins

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

Video - 00:05:49 mins

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

Video - 00:05:49 mins

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

Video - 00:15:22 mins

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

Video - 00:24:05 mins

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

Video - 00:17:33 mins

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

Video - 00:07:21 mins

06: Zoom Meetings to know everyone

Zoom Meeting No. 1

Video - 00:45:50 mins

07: File Formats

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

Video - 00:55:08 mins

08: VScode installation

VScode installation and other software installation methods in Linux mint

Video - 00:10:41 mins

09: Conda environments for Bioinformatics

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

Video - 00:19:49 mins

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

Video - 00:08:30 mins

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

Video - 00:03:21 mins

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

Video - 00:32:15 mins

10: git and gitHub

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

Video - 00:10:08 mins

11: R and RStudio

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

Video - 00:06:59 mins

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

Video - 11:55:37 mins

12: Linux Tool installation and use for Bioinformatics

Linux tips and updates about software use in bioinformatics

Video - 00:08:01 mins

Tools installation and use | grabseqs and sequences download from NCBI

Video - 00:36:04 mins

Download raw data from a manuscript from NCBI

Video - 00:03:45 mins

Downloading raw data using terminal and other commands

Video - 00:05:18 mins

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

Video - 00:04:54 mins

Video - 00:04:19 mins

13: Sequencing Technologies

Seuencing Technologies

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

14: Quality Control of Short Reads

Video - 00:39:23 mins

15: DNA and DNA sequencing

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

Video - 00:33:15 mins

Important Guide about sequencing technology

Video - 00:04:15 mins

Sequencing workflow and fastq files | zipped vs. unzipped files

Video - 00:10:35 mins

Bases vs. Base pairs in genome sequencing

Video - 00:04:44 mins

16: Genes and Genome

Difference between Genes and Genomes

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

Video - 00:13:47 mins

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

Prokaryotes or unicellular organisms

Video - 00:10:27 mins

Eukaryotes or Multicellular organisms

Video - 00:08:31 mins

Prokaryotes vs. Eukaryotes Major differences

Video - 00:09:19 mins

Prokaryotic genome structure

Video - 00:11:40 mins

How to calculate GC content in a genome?

Video - 00:01:27 mins

Eukaryotic genome structure | Exons vs. Introns

Video - 00:14:07 mins

Genome Size Comparison Prokaryotes vs. Eukaryotic genomes

Video - 00:02:33 mins

Prokaryotic genes vs. Eukaryotic Genes structures

Video - 00:02:54 mins

Why should you start learning from prokaryotic genomes? | Bioinformatics

Video - 00:06:28 mins

Resources and Databases for Prokaryotic & Eukaryotic Bioinformatics

Video - 00:02:17 mins

Tools for Prokaryotic vs. Eukaryotic Bioinformatics analysis

Video - 00:02:21 mins

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

Video - 00:04:25 mins

Complete Guide with Notes

Quizzes for Practice _ Bioinformatics ka chilla

Quizzes-01

Video - 00:02:12 mins

Quiz No. 1: Linux and Conda Quiz

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

16S rRNA gene and its importance for Microbial Ecology

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

Video - 00:36:46 mins

What is taxonomy?

Video - 00:01:29 mins

Levels of Taxonomy for Bacteria | Understanding Classification Theory with Examples

Video - 00:20:45 mins

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

Video - 00:43:19 mins

19: VScode, Git, GitHub, Markdown

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

Video - 00:11:17 mins

VScode experties | files, folders, interface, and settings

Video - 00:10:23 mins

VScode extensions

Video - 00:07:27 mins

Version control systems for coding and git

Video - 00:16:47 mins

Git installation

Video - 00:01:33 mins

Git CheatSheet

Git with terminal | local repository commands

Video - 00:22:55 mins

Git with VScode for local repository making and tracking changes

Video - 00:04:56 mins

hidden folder (.git ) and reseting repo

Video - 00:01:02 mins

Git and GitHub using VScode to sync and use online repo

Video - 00:12:17 mins

Git cloning online public repositories with three methods

Video - 00:05:44 mins

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

Video - 01:11:23 mins

20: Whole Genome Sequencing (WGS) and Genome Assembly workflow | Bacteria/Archaea

Intro to whole genome sequencing and assembly

Video - 00:27:24 mins

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

Video - 00:36:36 mins

Extract raw reads from NCBI SRA using grabseqs

Video - 00:22:01 mins

Genome assembly workflow summary so far

Video - 00:04:08 mins

raw reads and meta-data exploration

Video - 00:07:56 mins

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

Video - 00:28:34 mins

Short reads only genome assembly workflow and plan

Video - 00:18:13 mins

Short reads only assembly quality control of short reads automation

Video - 00:30:48 mins

Short reads genomes assembly guide and limitations with repeat regions

Video - 00:26:34 mins

fastqc quality report reading

Video - 00:20:49 mins

fastp use for read processing and trimming

Video - 00:27:07 mins

SPAdes as short reads assembler

Video - 00:13:36 mins

SPAdes output files for short reads only assembly

Video - 00:04:16 mins

Read spades output files and folders to make sense

Video - 00:13:24 mins

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

Video - 00:54:57 mins

Task to use QUAST for quality check of genomes by yourself

Video - 00:00:59 mins

QUAST for quality evaluation | QUAST Part-1/2

Video - 00:07:51 mins

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

QUAST outputs and reading results

Video - 00:13:58 mins

use BUSCO as genome assembly quality check | A-Z

Video - 00:22:55 mins

Types of genome assemblies based on quality metrics

Video - 00:11:20 mins

Tips to improve genome assembly quality

Video - 00:08:28 mins

Genome annotation with Prokka and Bakta

Video - 00:30:43 mins

Installation and analysis script is available on github

Video - 00:01:58 mins

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

Video - 01:14:08 mins

Results of Unicycler for Hybrid Genome Assembly

Video - 00:17:36 mins

Find plasmids in a genome using plassembler

Video - 01:31:24 mins

AMR genes and mobile genetic elements | ABRicate and geNomad

Video - 00:13:42 mins

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

Video - 00:29:55 mins

Whole Genome Sequencing and Genome assembly | Summary

Video - 00:01:26 mins

Tips to run script step by step for whole genome assembly

Video - 00:06:31 mins

Genome taxonomy and script

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

Video - 00:34:17 mins

Average Nucleotide Identity ANI score and cutoffs for novel species

Video - 00:12:00 mins

Reading Materials

Quiz Whole Genome Sequencing and Assembly

Video - 00:02:49 mins

CompareM2 for genome assembly comparison | Big Pipeline

01-RNAseq or Transcriptomics | Introduction and plan

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

Video - 00:22:46 mins

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

Video - 00:00:30 mins

03-RNAseq sessions and tips for learning

Video - 00:02:16 mins

04-Central dogma and Transcriptomics

Video - 00:02:11 mins

05-Isolate vs. Community of organisms

Video - 00:02:19 mins

06-Cultured vs. Uncultured Organisms

Video - 00:02:20 mins

07-What is a genome?

08-Key Aspects of a Genome important for Omics

Video - 00:06:46 mins

09-Omics Techniques to learn as a Bioinformatics and Transcriptomics

Video - 00:08:40 mins

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

Video - 00:12:58 mins

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

Video - 00:01:15 mins

12-Types and Methods of Transcriptomics Analysis

Video - 00:13:19 mins

13-Bulk RNAseq example in detail

Video - 00:06:08 mins

14-Steps involved in RNAseq experiments

Video - 00:01:56 mins

15-Study Design in RNAseq experiment Step-1

Video - 00:09:58 mins

16-Library preparation and sequencing Step-2

Video - 00:01:18 mins

17-Deeper sequencing or More replicates for RNAseq experiment

Video - 00:17:49 mins

18-Read length for sequencing for illumna

Video - 00:02:48 mins

19-Single End vs. Paired End Reads from Illumina

Video - 00:11:44 mins

20-Two important costs for RNAseq Experiments

Video - 00:02:17 mins

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

Video - 00:10:28 mins

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

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

Video - 00:02:25 mins

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

Video - 00:06:16 mins

25-FASTA file format vs. FASTQ

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

Video - 00:04:46 mins

27-RNAseq workflow for Bioinformatics

Video - 00:06:24 mins

28-RNAseq pipelines for Transcriptomics analysis

Video - 00:11:22 mins

29-READemption RNAseq pipeline installation step by step guide

Video - 00:17:16 mins

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

Video - 00:21:59 mins

31-Task for RNAseq analysis for Students

Video - 00:01:45 mins

32-Handling errors for installations and run for READemption

Video - 00:08:27 mins

33-Methods to prevent errors for READemption

Video - 00:08:35 mins

34-READemption scripts are online on github

Video - 00:03:19 mins

35-Read count & Normalization for RNAseq

Video - 00:16:15 mins

36-RPKM FPKM TPM and Log2FoldChange in RNAseq

Video - 00:14:25 mins

37-READemption Output and results of RNAseq for interpretation

Video - 00:22:57 mins

38-DESeq output files reading and understanding

Video - 00:10:04 mins

39-Save your data first and then work on it

Video - 00:02:15 mins

40-READemption use for future analysis

Video - 00:01:40 mins

41-RNAseq analysis on a publication data for Archaea

Video - 00:07:01 mins

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

Video - 00:23:54 mins

43-Task for Students

Video - 00:01:20 mins

44-Pipeline successfully worked for the analysis

Video - 00:02:12 mins

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

Video - 00:19:20 mins

46-IGB to read coverage files for each RNAseq outputs

Video - 00:15:23 mins

47-Docker with DockerHub for any bioinformatics tool

Video - 00:14:13 mins

48-Docker uninstallation issue and bugs

Video - 00:06:11 mins

49-Google Antigravity for Bioinformaticians and RNAseq + Docker

Video - 00:09:26 mins

50-Install Docker for Bioinformatics Tools

Video - 00:14:21 mins

51-Use docker for RNAseq analysis with READemption

Video - 00:15:59 mins

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

Video - 00:04:45 mins

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

Video - 00:04:07 mins

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

Video - 00:05:35 mins

55-genome fasta and gff files for the sample Organisms

Video - 00:02:58 mins

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

Video - 00:10:19 mins

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

Video - 00:09:13 mins

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

Video - 00:10:38 mins

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

Video - 00:03:41 mins

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

Video - 00:09:30 mins

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

Video - 00:16:05 mins

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

Video - 00:03:13 mins

63-rRNAs are bad for RNAseq analysis, really?

Video - 00:10:11 mins

64-Publication ready plots for RNAseq analysis outputs from READemption

Video - 00:19:48 mins

65-Task for Students for RNA analysis from a Paper

Video - 00:01:49 mins

66-RNAseq visualization Application for READemption output

Video - 00:50:28 mins

67-Functional Enrichment Analysis Application is ready

Video - 00:21:57 mins

68-Application deployment on streamlit cloud

Video - 00:04:22 mins

69-RNAseq course completed

01-Introduction to Pangenomics

22a: Pangenomics

Video - 00:06:08 mins

02 -Tools and Pipelines for Pangenomics analysis for prokaryotes

Video - 00:09:53 mins

03 -Task for Pangenomcis run Panaroo analysis

Video - 00:03:07 mins

04-Pangenomics Workflow and the importance of generating pangenomes

Video - 00:05:02 mins

05-Core vs. Accessory Pangenomes

Video - 00:22:24 mins

06 -Pangenomics key concepts

Video - 00:08:52 mins

07-PanExplorer for Pangenome Analysis

Video - 00:17:02 mins

08-PanExplorer results and report reading for manuscripts

Video - 00:16:11 mins

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

Video - 00:25:14 mins

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

Video - 00:02:21 mins

11-Panaroo Results and understanding of outputs

Video - 00:08:29 mins

12-Cytoscape for network visualization of pangenome

Video - 00:04:19 mins

13-Task to run Anvio workflow for Pangenome analysis

Video - 00:05:44 mins

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

Video - 00:09:09 mins

22b: Anvio for Pangenomics

01-Installation of Anvio Pipeline | Anvio for Pangenomics

Video - 00:28:40 mins

02-Steps to perform Pangenome analysis using ANVIO pipeline

Video - 00:14:45 mins

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

Video - 00:33:03 mins

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

Video - 00:13:57 mins

05 -Task for students to do Pangenome analysis

Video - 00:00:42 mins

06-Graphical User Interface of ANVIO Pangenome Main Menu

Video - 00:20:44 mins

07-Anvio pangenome BINs and Options

Video - 00:16:42 mins

08-Dendograms and layes in Anvio pangenome

Video - 00:03:17 mins

09-Search function of Anvio and layers in Anvio Pangenome

Video - 00:16:19 mins

10-Legends in Anvio Pangenome

Video - 00:02:16 mins

11-Anvio ANI using pyANI and layers on Pangenome

Video - 00:16:04 mins

12 -Split pangenome parts from main pangenome

Video - 00:05:16 mins

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

Video - 00:04:32 mins

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

Video - 00:00:52 mins

15-Ideas for Pangenome analysis

Video - 00:01:48 mins

16-Important key ideas for Pangenome manuscripts

Video - 00:01:38 mins

17-Pangenomics strategies for complete studies and papers

Video - 00:07:35 mins

18-Step 1: QC before pangenomics

Video - 00:09:11 mins

19-Step 2: Define biological questions clearly for pangenomics

Video - 00:16:58 mins

20-Step 3: Inspect core vs. Accessory vs. Sigleton in pangenome

Video - 00:08:39 mins

21-Step 4: Build a phylogenomics view of pangenome

Video - 00:05:25 mins

22-Step 5: Functional Enrichment Analysis and Annotation

Video - 00:10:28 mins

23-Step 6: Identify clade specific gene clusters in pangenome

Video - 00:02:03 mins

24-Step 7: Explore Genome organization and synteny

Video - 00:03:23 mins

25-Step 8: Check for Mobile Genetic Elements

Video - 00:02:17 mins

26-Step 9: Test pangenome Openness

Video - 00:01:56 mins

27-Step 10: Link Meta data to presence absence matrix of genes

Video - 00:01:45 mins

28-Step 11: Pangenome and ANI score

Video - 00:02:08 mins

29-Step 12: Look for Evidence of Horizontal gene transfer

30-Step 13, 14, 15: Analysis to results reporting

Video - 00:03:49 mins

31-Step 1 to 15: Summary of Strategies for Pangenome Analysis and Reporting in papers

Video - 00:01:28 mins

32-Practical Guide for Pangenome Analysis in guided steps

Video - 00:02:19 mins

33-Most common mistakes in Pangenome analysis and Strategies to overcome

Video - 00:02:51 mins

34-Task for Students for ANVIO Pangenomics analysis

Video - 00:01:45 mins

23: CAZyme (Carbohydrate Active Enzymes) and PULs (Polysaccharides Utilization Loci) Analysis

01-What are CAZymes?

Video - 00:04:55 mins

02-Types of CAZymes based on functions

Video - 00:05:39 mins

03-Why CAZymes are important for biologists?

Video - 00:10:22 mins

04-Steps to do CAZyme analysis and tools

Video - 00:05:22 mins

05-Installation of dbcan for CAZyme analysis

Video - 00:05:03 mins

06-CAZyme analysis complete tutorial on Linux

Video - 00:30:37 mins

07-CAZyme Analysis figure ideas for Publications

Video - 00:01:38 mins

08-CAZyme and PULs analysis with two different genomes and plotting the results for Manuscript

Video - 00:13:29 mins

24: Secretion Systems in Bacteria (Type-I to Type-VI and Type-IX)

01-Genomes to Pangenomes and AMR genes plus much more

Video - 00:09:43 mins

02-Secretion systems in Bacteria introduction

Video - 00:16:06 mins

03-T1SS to T6SS and T9SS in details

Video - 00:17:57 mins

04-Bioinformatics tools for secretion systems analysis and detection

Video - 00:02:31 mins

05-Research projects based on Secretion systems in Bacteria

Video - 00:11:45 mins

06-Linux for Secretion systems with MacSyFinder and TXSScan complete guide

Video - 00:16:42 mins

07-Task for students for Secretion systems

08-TFFscan | CONJscan | CasFinder systems in a genome

Video - 00:10:20 mins

25: CRISPR_Cas, CONJscan and TFFscan systems in Bacterial Genome

TFFscan | CONJscan | CasFinder systems in a genome

Video - 00:10:20 mins

26: Amplicon Sequencing (Microbial Ecology)

01-Microbial Ecology and 16s rRNA sequence analysis

Video - 00:14:30 mins

02-16S rRNA gene and Amplicon sequencing analysis using QIIME2

Video - 00:11:23 mins

03-QIIME2 installation in linux with conda giving errors

Video - 00:14:29 mins

04-Installation of QIIME2 using conda and mamba in linux (Working fine)

Video - 00:07:35 mins

05-Task for Students

Video - 00:00:50 mins

06-QIIME2 analysis of real data as an example

Video - 00:09:48 mins

07-Metadata to visualization as QIIME2 artifact

Video - 00:03:28 mins

08-Jupyter notebooks are much better than CLI for QIIME2 analysis

Video - 00:05:30 mins

09-Importing data in QIIME2 to use for analysis

Video - 00:07:48 mins

10-Demultiplexing the data in QIIME2 for amplicon sequencing

Video - 00:08:49 mins

11-Summary of next steps

Video - 00:12:18 mins

12-DADA2 for denoising the samples

Video - 00:29:08 mins

13-Deblur for denoising the samples

Video - 00:16:47 mins

14-Feature Tables summary and representative sequences

Video - 00:10:25 mins

15-Generate Phylogenetic trees after aligning the data

Video - 00:04:46 mins

16-How to view phylogenetic trees in iOTL?

Video - 00:03:14 mins

17-Assignment alert before next lecture

Video - 00:02:51 mins

18-Alpha vs. Beta diversity introduction and need in Amplicon sequencing

Video - 00:33:17 mins

19-Alpha diversity Richness vs. Evenness

Video - 00:04:10 mins

20-Alpha diversity Metrics and Methods

Video - 00:20:07 mins

21-List of Alpha diversity Metrics in Qiime2

Video - 00:01:55 mins

22-Beta diversity methods and metrics

Video - 00:23:09 mins

23-Assignment or task alert

Video - 00:02:05 mins

24-PCA | Principal Component Analysis | Theory

Video - 01:12:44 mins

25-PCA | Principal Component Analysis | Case Study in Python

Video - 00:30:39 mins

26-PCA vs. PCoA analysis for Beta-diversity analaysis

Video - 00:23:37 mins

27-Alpha- and Beta-Diversity Core Metrics in one code with optimization with group significances

Video - 00:34:30 mins

28-Assignment Alert | Very important one

Video - 00:00:51 mins

29-Group Significance in Alpha-diversity continuous variables with metadata

Video - 00:04:44 mins

30-PERMANOVA Analysis for Beta-diversity metrics and Meta-data using QIIME2

Video - 00:16:51 mins

31-PCoA plots to view and understand beta diversity using QIIME2

Video - 00:10:59 mins

32-Alpha-rarefaction plots and ASVs with sequencing depth

Video - 00:11:37 mins

33-Taxonomic analysis using Machine Learning

Video - 00:09:10 mins

34-Taxonomy in Amplicon sequencing is an important step

Video - 00:07:41 mins

35-Taxonomy analysis using QIIME2 using classifier training with ML

Video - 00:24:37 mins

36-Taxonomy analysis in QIIME2 using pre-trained SILVA database classifier

Video - 00:10:14 mins

37-Differential Abundance analysis using ANCOM-BC in QIIME2

Video - 00:18:34 mins

38-Next steps in Amplicon Sequencing analysis using QIIME2

Video - 00:02:22 mins

39-Complete A-Z Guided Tutorial of Microbial Ecology Analysis using QIIME2 for Amplicon sequencing

Video - 01:01:03 mins

40-Impact of Amplicon sequencing analysis and figure interpretation

Video - 00:19:15 mins

41-16S vs. 18S vs. ITS analysis

Video - 00:17:02 mins

42-Tools for Amplicon sequence analysis

Video - 00:07:16 mins

43-Amplicon sequence analysis from a published article

Video - 00:51:14 mins

44-Download raw data based on publication

Video - 00:19:20 mins

45-Code is available in this lesson

Video - 00:00:15 mins

46-QIIME2 for ITS and Github copilot

Video - 00:16:45 mins

47-Amplicon sequence with ITS completed

Video - 00:03:47 mins

27-Metagenomics A-Z

01-Metagenomics | introduction for beginners

Video - 00:20:56 mins

02-Key Terminologies and Analysis pipeline in Metagenomics

Video - 00:06:10 mins

03-QIIME2 MOSHPIT installation and tools for metagenomics

Video - 00:16:08 mins

04-Assignment for Students

Video - 00:02:28 mins

05-Understanding Metagenomics Made Easy

Video - 00:06:10 mins

06-Metagenomics with MOSHPIT QIIME2 workflow understanding

Video - 00:14:12 mins

07-Raw Reads to Contigs building

Video - 00:10:27 mins

08-Understanding De Bruijn Graphs in the Best Possible Way

Video - 00:22:28 mins

09-Assembly QC

10-Read Mapping for Metagenomics

Video - 00:03:43 mins

11-Contig Binning to MAGs reconstruction

Video - 00:06:26 mins

12-MAGs QC and MAGs filtering

Video - 00:01:21 mins

13-MAGs Dereplication

Video - 00:03:04 mins

14-Taxonomic Classification

Video - 00:02:00 mins

15-MAGs abundance estimation

Video - 00:02:43 mins

16-Taxa Barplots for Taxa understanding

Video - 00:00:31 mins

17-Summary, common mistakes and Conclusion

Video - 00:07:13 mins

18-Hands on Tutorial for MAGs reconstruction using QIIME2 MOSHPIT

Video - 00:29:09 mins

19-Assignment for Students

Video - 00:00:42 mins

20-Exploring results of MAG reconstruction tutorial and what we actually need for paper

Video - 00:16:25 mins

21-Cocoa Fermentation tutorial understanding and start

Video - 00:04:02 mins

22-COCOA Fermentation Tutorial Understanding of Data and treatments

Video - 00:06:02 mins

23-Download raw data with ENA using SRR list for cocoa fermentation if we need to use RAW reads

Video - 00:09:24 mins

24-Anvio for metagenomics Installation of Anvio Pipeline

Video - 00:28:40 mins

25-Anvio for Metagenomics and shortreads QC

Video - 00:30:06 mins

26-Parallel computation and Anvio for Metagenomics

Video - 00:23:44 mins

27-QC reports of reads

Video - 00:02:14 mins

28-How did I select Samples subset?

Video - 00:01:44 mins

29-Assignment Task for Students

Video - 00:01:22 mins

30-Scripts used till now for Metagenomics and Data Retrieval

31-Megahit Co-Assembly is ready to view and check

Video - 00:10:11 mins

32-QC Reports and MultiQC Reports

Video - 00:04:57 mins

33-Co-assembly QC with Metaquast and graph with Bandage

Video - 00:11:36 mins

34-Metaquast error due to insufficient RAM

Video - 00:04:42 mins

35-QUAST and MetaQUAST worked with fewer references

Video - 00:05:55 mins

36-Optimizing Metaquast: RAM issues killed the process

Video - 00:01:05 mins

37-Metaquast is almost working properly

Video - 00:01:14 mins

38-Metaquast worked fine and now we can see results

Video - 00:01:14 mins

39-Anvio reformat fasta files of contigs before mapping

Video - 00:03:36 mins

40-Reformatting and Indexing done Mapping started with parallel computation

Video - 00:03:39 mins

41-Mapping done and results are ready

Video - 00:01:18 mins

42-sorting and indexing of bam files

Video - 00:02:32 mins

43-sorting completed and results are here

Video - 00:00:45 mins

44-Creating ANVIO compatible database of contigs

Video - 00:01:06 mins

45-Run HMMs on contigs with results

Video - 00:02:40 mins

46-Display contigs stats in iteractive view of Anvio

Video - 00:02:41 mins

47-Profiling of all samples using Anvi'o

Video - 00:08:31 mins

48-Profiling completed and results are here

Video - 00:02:23 mins

49-Merge all profiles using this command

Video - 00:02:33 mins

50-Merging completed but with warnings

Video - 00:01:38 mins

51-What Merging Profiles Means?

Video - 00:00:36 mins

52-Binning and binning tools available for metagenomics and their installation outside Anvio env

Video - 00:03:51 mins

53-Prepare for binning tools outside Anvio

Video - 00:02:55 mins

54-Metabat2 binning algorithm and its outputs

Video - 00:01:34 mins

55-Concoct as a binning algorithm: Script and output

Video - 00:02:11 mins

56-MaxBin2 binning algorithm script and output comparison

Video - 00:03:04 mins

57-Prepare outputs of all three binning algorithms for DAS Tool

Video - 00:08:22 mins

58-DAS Tools to combine outputs of all three script and runtime

Video - 00:05:43 mins

59-DAS tool output and files

Video - 00:02:11 mins

60-DAS Tools output import in Anvio and summary details of final Bins

Video - 00:17:54 mins

61-MAG quality Estimation after binning

Video - 00:07:29 mins

62-All binning tools and MAGs quality estimation summaries

Video - 00:14:41 mins

63-Taxonomic classification of MAGs using Anvio SCG Taxonomy Script is provided

Video - 00:06:10 mins

64-Data visualization of Taxonomy

Video - 00:01:35 mins

65-Data Visualization and publication ready figures from MAGs

Video - 00:08:29 mins

66-Assign Taxonomy to Sample Metadata

Video - 00:03:31 mins

67-Selection of High Quality HQ MAGs

Video - 00:03:36 mins

68-Export fasta files of each MAG based on Quality and binning tool

Video - 00:02:51 mins

69-Run Functional Annotation and Taxonomy for contigs to know who is there and what they are doing

Video - 00:03:42 mins

70-We have learned so far these topics

Video - 00:03:38 mins

71-PC management guide for Bioinformaticians using threads cores and ram with SSD

Video - 00:22:14 mins

72-Anvi’o tutorials are important for everyone for OMICs

Video - 00:03:17 mins

73-Simple read recruitment exercise using Anvio pipeline

Video - 00:44:50 mins

74-Assignment task for students

Video - 00:1:20 mins

75-Further tips and the use of the MetaWRAP pipeline for metagenomics analysis

Video - 00:05:52 mins

76-Further analysis of MAGs are similar to WGS analysis

Video - 00:22:52 mins

77-Limitation of doing metagenomics analysis in Pakistan or abroad

Video - 00:09:45 mins

78-Assignment for students

Video - 00:00:48 mins

79-What are we learning from now on