stephenturner/oneliners resource

Health v2 · maintenance only

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2026 stars · 524 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

A curated collection of useful bash one-liners for bioinformatics, covering awk, sed, sort/uniq/cut, find/xargs/GNU parallel, seqtk, and GFF3 annotation tricks. It is a reference document rather than software, with some generally useful shell aliases included.

Use cases

• extract and filter columns from bioinformatics text files with awk
• manipulate FASTA and sequence files from the command line
• learn awk and sed one-liners for genomic data processing
• find bash commands to parse GFF3 annotation files
• deduplicate and summarize tabular data in the shell
• set up useful bashrc aliases for bioinformatics work

When to choose

• you work with genomic or bioinformatics text data on the Unix command line
• you want a quick reference of proven awk/sed one-liners instead of writing scripts
• you need to process FASTA, BED, or GFF files without installing heavy tools

When to avoid

• you need a maintained software tool or library with a license and releases
• you want a GUI or pipeline framework rather than copy-paste shell commands
• you need Windows-native tooling without a Unix-like shell

Facets

learning-resource · maturity maintenance

developer-tools cli data-science bioinformatics developer-tools cli cheatsheet bash awk sed one-liners genomics reference command-line linux macos

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