Unix essentials for NGS bioinformatics

Learn how wc reports lines, words, and characters with different options. Use diff to compare two files line by line, highlighting exact differences and showing when files are identical.

Use the paste command to join two files horizontally by default with tab separation, customize the delimiter with -d (for example pipe or comma), and support joining multiple files.

Learn how to use the Unix cut command to extract specific columns and ranges from annotation files, such as ids and numerical data, for bioinformatics data processing.

Explore grep basics for bioinformatics, including case sensitivity and -i for insensitive searches, -c to count matches, -f to read patterns from a file across files, and start/end pattern matching.

Explore the Unix file system, where directories are files and a single root underpins the directory tree. Learn absolute and relative paths and use cd to move between locations.

Learn sorting and deduplication with unix sort and uniq: sort by column one or two, reverse order using field separators, save output, and count, show duplicates, or show unique lines.

Explains how piping in unix passes output from one command to another, enabling sorting and extracting nonredundant annotation information from a two-column transcript file, and saving results with redirection.

Learn how Unix streams manage data with standard input, standard output, and standard error, and how to pipe and redirect to files to build robust bioinformatics workflows.

Use chmod to change file permissions for user, group, and others. Create links with ln to files or folders, simplifying access and data processing.

Explore the sed command in Unix for substitution, insertion, and deletion to process data without opening files. Learn s/pattern/replacement/, the global g option, line addressing, and deleting lines.

Master the tr command to transform text, convert lowercase to uppercase (and back), delete digits, extract digits, and convert spaces to single spaces using pipes in unix and ngs bioinformatics.

Build a terminal pipeline to convert fastq to fasta sequences, counting reads, extracting headers with grep, removing dash and blank lines, and replacing the plus line with the greater symbol.

Learn a terminal pipeline to convert multi-line fasta sequences into a single-line format by adding header reference points, joining lines, removing unwanted characters, and splitting into sequence entries for analysis.

Move from command to scripts in Unix essentials for NGS bioinformatics, enabling reproducible analyses with pattern matching using ?, {}, [], square brackets, backslash escapes, and grep-based counting.

Learn how to create and manipulate Unix variables, store strings or numbers, access values with dollar signs or curly braces, extend or extract parts, and delete variables with unset.

Learn to use Unix arrays to store multiple values (DNA, RNA) in a single variable, retrieve elements by index, print them, and script terminal tasks for NGS bioinformatics workflows.

Use a Unix subshell to run commands, using parentheses or backticks to store results in a variable, such as counting sequences from a file.

Explore Unix loops to automate data processing, including while and for loops, handling large file sets, and counting sequences by piping, grep, and cat.

Learn how to install software in unix-based bioinformatics workflows, including precompiled executables and installation from source code, with steps for permissions, configuration, linking, dependencies, and using fast qc.

Demonstrates building a data-processing pipeline for ingesting, downloading fastq files with wget, performing fastqc and multiqc quality assessment, and applying trimming and quality control before mapping, assembly, and downstream analysis.

Follow a three-step bioinformatics pipeline for phylogenetic analysis. Align sequences with cluster w, construct tree with Feynman, and identify sites of evolution using code AML.