Learn Genome Assembly & Annotation in Prokaryote & Eukaryote

Learn Linux for bioinformatics by mastering Ubuntu basics, command line workflows, scripting, and package management with Conda and apt, plus blast and Hisat2 for alignment.

Install and configure the Windows Subsystem for Linux on Windows, set up Ubuntu, manage distributions with PowerShell and the Microsoft Store, and run GUI apps via X11.

Navigate the Linux file system to organize bioinformatics data by understanding the root, absolute and relative paths, and basic commands like ls, pwd, and cd.

Master linux commands for file and directory management, including copy, move, delete, and view operations (ls, cd, mkdir, cp, mv, rm, head, tail) to organize sequencing data and automate workflows.

Master viewing, editing, and processing genomic data in Linux with grep, awk, and other text tools to extract fasta headers, filter gff/gtf entries, and count sequences.

Learn how to install and use conda with Miniconda or Anaconda across Linux, Windows, and macOS, including terminal commands and basic environment setup.

Understand how genome assembly reconstructs a genome from fragmented reads using short and long reads, with algorithms like overlap-layout-consensus, de Bruijn graphs, and greedy algorithms to form contigs and scaffolds.

Explore short read sequencing by Illumina, delivering high-throughput, accurate data for whole genome sequencing, transcriptomes, and metagenomics, while limited by short reads spanning repetitive regions and assembly challenges.

Retrieve public short read data for Mycobacterium ulcerans, download paired-end Illumina fastq files with wget, and prepare quality checks for genome assembly.

Install and verify essential tools, including FastQC and MultiQC, prepare data directories, perform quality control and trimming of short reads, then assemble with SPAdes and visualize with Bandage.

Assemble short reads with spades to produce contigs and scaffolds, and visualize the results with Bandage. Prepare visualization on wsl2/x11 before moving to long-read assembly with flye.

Learn how long read sequencing with Oxford Nanopore and PacBio enables real-time analysis and better resolution of structural variations and repetitive regions, while balancing throughput and cost with short reads.

Download SRA nanopore fastq data and set up a conda environment, then install fly for genome assembly and trimming, perform quality checks, and plan post-assembly validation.

Assess long-read quality with fast qc, trim adapters if needed, generate trimmed fastq, and prepare for assembly with fly to produce reliable nanopore-based genome assemblies.

Assemble long Nanopore reads into contigs and visualize the assembly graph with bandage. Explore using the fly tool, review assembly.fasta and gfa outputs, and note about 69 contacts.

Learn how to convert assembled genomes into labeled features with genome annotation, differentiate structural and functional annotation, and apply prokaryote and eukaryote pipelines for gene prediction.

Learn to rapidly annotate prokaryotic genomes with Prokka, a fast pipeline that integrates Aragorn and BLAST for structural and functional annotation.

Learn how to perform prokaryotic genome functional annotation using blast, build a UniProt blast database, run protein blast against it, and interpret tsv results for gene IDs and protein functions.

Predict protein domains in prokaryotes by running hmmer against the hammer and PFM databases to identify domain IDs and assign protein families for domains within genomes.

Annotate eukaryotic genomes with Augustus to predict gene structures and intron and exon boundaries, integrating rna-seq and protein evidence.

Annotate eukaryotic genomes by building a UniProt-based blast database, running Augustus protein queries, predicting domains with hammer against the PFM database, and validating results with quality metrics.