Linux for Bioinformatics: Beginner to Advanced

Learn core Linux command lines, including touch for creating files, mkdir for directories, and cat for displaying and concatenating file contents, with practical tips like redirection, options, and command history.

Learn to use pwd to display the current directory and cd to navigate with absolute and relative paths, including home tilde, parent directory (..), and creating directories.

Learn to navigate the linux filesystem with cd using parent, home, and directory shortcuts, and use absolute and relative paths to create a linux course folder with subfolders and files.

Learn how to list directory contents with ls, using -l, -h, and -a for permissions, ownership, human-readable sizes, and hidden files, plus wildcards to match patterns.

Learn how to set Linux permissions for files and directories using chmod, assign read, write, and execute rights to owner, group, and others, and verify with ls -l.

Learn how to change file permissions with numeric mode using chmod, interpreting digits for user, group, and others, and compare numeric vs symbolic chmod methods.

master the rm command to remove files and directories safely, using options like -r, -f, and -i to control recursive deletion, force removal, and interactive confirmations.

Move or rename files and directories with mv by specifying a source and destination. Use relative paths and the i option to prompt before overwriting.

use the cp command to copy files and directories, leaving the original intact; use -R for directories and -i to prompt before overwriting.

Search patterns across files or streams with grep, using options, patterns, and file names. Learn case-insensitive and inverted searches with -i and -v, anchors like ^, and basic regular expressions.

Learn sed, the stream editor, to substitute text, replace patterns with the s command, and delete lines on the command line using flags like g.

Use the sort command to arrange text lines in a file in alphabetical or numerical order, with -r for reverse, -u for unique lines, and -n for numeric sorting.

Explore how the unique command removes adjacent duplicates and counts occurrences with -c, -d, and -u, illustrated by a fruits file.

Extract fasta headers from a multi-fasta file with Linux command line, remove the '>' symbol, sort IDs ascending, and output a final unique list of sequence IDs using piping.

Use the Linux command line to extract sequence headers from a multiphasic file and save them as a text list of IDs, describing reads and quality scores.

Explore the shell and Bash on Linux, and learn to interact with the OS via the command line, automate tasks with Bash scripting, and use variables, loops, conditionals, and functions.

Learn to write and run bash scripts, starting with the shebang, implement for loops, use head and tail to process multiple files, and set executable permissions for ./script.

Understand how a variable stores values in bash, using the file name variable in a for loop to substitute names like basilisk, spyridium, and unicorn in commands.

Master vim on the command line to write, save, and execute bash scripts: install vim, enter insert mode, add shebang, save with wq, chmod to 774, and run with ./script.

Learn to write bash scripts with interactive prompts, using echo and read to store user input in variables and print personalized greetings in case one.

Create a simple calculator with a bash script that prompts for two numbers, computes and displays addition, subtraction, multiplication, and division results.

Nano offers a user-friendly text editor with a simple interface for editing configuration files and writing scripts. Demonstrates saving with Ctrl O, exiting with Ctrl X, and making scripts executable.

Learn the linux if statement to run commands based on a condition, test file existence with -e, and check file types with -f, using then, else, and fi.

Explore bash if statements with prompts, read, and string comparisons, then build a simple login script that compares a user input to a stored password and exits accordingly.

Demonstrates a bash if statement validating a user-entered DNA sequence with a regex pattern for DNA characters (A, C, T, G) in any case and prints valid or invalid.

Showcases bash for loops to iterate over fasta files, extract and sort header lines, remove duplicates, and write sorted headers to files named after the originals with headers to text.

Learn to count leucine occurrences in a protein sequence using a for loop in bioinformatics, iterating characters with grep, updating a counter, and printing the final total once.

Explore how the bash while loop repeatedly executes a code block while a boolean condition stays true, using a simple script that prints hello world five times.

Use a bash while loop to read each sequence from a text file with read -r, printing and analyzing DNA sequences such as GC content and motifs.

Explore how a while loop processes a fasta file to produce reverse complements of DNA sequences while preserving headers. Read headers and sequences, reverse, and write results to output file.

Develop bioinformatics scripting by starting small, mastering foundational concepts, and using online tutorials and forums to collaborate, adapt, and learn through hands-on exploration.

Explore the Muscle tool for multiple sequence alignment in both GUI and CLI to gain a comprehensive, flexible understanding, emphasizing automation, reproducibility, scalability, and transferable bioinformatics skills.

Compare biological sequences to identify similarities and conserved patterns using pairwise and multiple sequence alignment, global and local approaches, with tools such as EMBOSS, Clustal Omega, MAFFT, MUSCLE, and BLAST.

Explore multiple sequence alignment using Muscle to align HIV-1 envelope glycoprotein sequences from five strains. Benchmark tools like Clustal Omega to compare output formats and conservation patterns.

Perform a command-line multiple sequence alignment with muscle, from fetching sequences to exporting cluster W or html outputs. Apply the workflow to functional annotation, disease mutation analysis, and primer design.

Congratulate learners on completing the course and invite feedback on this course and upcoming offerings. Express gratitude for the wonderful teaching and learning experience, and wish learners a bright future.