Classic Bioinformatics Software

Bioinformatics

Software

How foundational command-line tools work, when to use them, and how they fit together.

Modified

October 16, 2026

Sequence alignment

Planned: BWA, Bowtie2, STAR, minimap2.

Genomic file operations

Planned: SAMtools, BCFtools, BEDtools, tabix, Picard.

Variant and feature analysis

Planned: GATK, Cell Ranger, MACS2 and related tools.

---
title: "Classic Bioinformatics Software"
description: "How foundational command-line tools work, when to use them, and how they fit together."
categories: [Bioinformatics, Software]
---

## Sequence alignment

Planned: BWA, Bowtie2, STAR, minimap2.

## Genomic file operations

Planned: SAMtools, BCFtools, BEDtools, tabix, Picard.

## Variant and feature analysis

Planned: GATK, Cell Ranger, MACS2 and related tools.