Linux Commands for Bioinformatics Cheat Sheet
A compact reference for everyday Linux commands, biological file inspection and useful command combinations.
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Download practical cheat sheets, workflow guides, templates and starter scripts designed to support bioinformatics learning and real data analysis.
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Build practical foundations with five useful resources for command-line work, sequence files, biological databases, RNA-Seq and project documentation.
A compact reference for everyday Linux commands, biological file inspection and useful command combinations.
Download PDFA quick visual guide to sequence records, quality scores and the roles of FASTA and FASTQ files.
Download PDFA practical guide to major biological databases and what each resource is best used for.
Download PDFA step-by-step reference from experimental design and FASTQ files to functional analysis.
Download PDFA reusable Markdown project template packaged as a ZIP for clear, reproducible documentation.
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Search free bioinformatics downloads including bioinformatics cheat sheets, workflow PDFs, templates, R scripts, Python scripts and reproducibility resources.
15 resources · Updated August 2026
A compact command-line reference covering common Linux commands, biological file inspection and practical command combinations used in bioinformatics.
Covers: navigation, file operations, grep, head / tail, pipes, redirection, FASTA counting and FASTQ inspection.
A quick visual reference explaining the differences between FASTA and FASTQ files, their structures and where they appear in bioinformatics workflows.
Covers: sequence records, quality scores and NGS reads.
A practical reference to SAM and BAM alignment files, common SAM fields and essential samtools operations.
Covers: SAM, BAM, FLAG, MAPQ, CIGAR, sorting and indexing.
A compact guide to the Variant Call Format including core fields, genotype codes and essential concepts used in variant analysis.
Covers: CHROM, POS, REF, ALT, QUAL, FILTER and genotype.
A practical guide to major biological databases and what each resource is best used for.
Includes: NCBI, GenBank, SRA, GEO, Ensembl, UniProt, PDB and ENCODE.
A step-by-step reference showing the major RNA-Seq workflow stages from experimental design and FASTQ files through differential expression and functional analysis.
Workflow: experimental design → FASTQ → QC → preprocessing → alignment / quantification → counts → differential expression → visualization → functional analysis.
A practical workflow guide covering read QC, reference alignment, BAM processing, variant calling, filtering, annotation and interpretation.
Workflow: read QC → alignment → BAM processing → calling → filtering → annotation → interpretation.
A high-level reference showing how whole-genome sequencing progresses from DNA and sequencing through alignment, coverage analysis, variant discovery and interpretation.
Workflow: DNA → sequencing → alignment → coverage → variant discovery → interpretation.
A practical single-cell workflow reference covering count matrices, QC, normalization, dimensionality reduction, clustering, marker analysis and cell annotation.
Covers: count matrices, QC, normalization, dimensionality reduction, markers and annotation.
An editable RNA-Seq sample metadata template for organizing conditions, biological replicates, batches, sequencing layout and experimental information.
Fields: sample_id, condition, biological_replicate, batch, read_layout, library_type, organism, tissue_or_cell_type, sex, time_point, sra_run and notes.
A reusable project documentation template for organizing biological questions, datasets, software environments, workflows, results and reproducibility information.
Inside the ZIP: an editable Markdown README project template.
A practical checklist covering data provenance, metadata, reference files, software versions, code, environments, statistics, figures and project documentation.
Review: data, metadata, references, versions, code, environments, statistics, figures and documentation.
An educational starter script for generating a volcano plot from differential-expression results containing gene, log2FoldChange and adjusted p-value columns.
Inside the ZIP: an R starter script. Requires R and ggplot2.
An educational PCA starter script for generating a two-dimensional PCA visualization from a numeric expression matrix.
Inside the ZIP: an R starter script. Requires R and ggplot2.
A lightweight educational Python utility that counts FASTA records and reports basic sequence-length statistics.
Outputs: sequence count, total residues / bases, shortest sequence, longest sequence, mean length and median length.
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From Reference to Practice
Use the reference resources to understand concepts, adapt templates and scripts to your own data, and document any changes you make.
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Connect each download with a tutorial, practice dataset, tool guide, learning path or course.
Use a cheat sheet for quick reference, follow a workflow guide, customize a template or explore a starter script while working with real biological data.
Bioinformatix provides hands-on training in bioinformatics, genomics, AI, machine learning, and sequencing data analysis. Learn through real-world projects, practical workflows, and industry-focused courses designed for students, researchers, and professionals.