Local-first genomics toolkit

Turn whole genome data into useful files, reports, and extracts.

WGS Extract CLI is a modern, scriptable command-line recreation of WGS Extract. It wraps common bioinformatics tools so you can inspect BAM/CRAM files, build consumer microarray files, call variants, extract Y/MT reads, manage references, and automate repeatable genome work.

Install the CLI Download the GUI Browse workflows Learn WGS basics

# Open Terminal, paste this line, then press Enter
$ curl -fsSL https://raw.githubusercontent.com/WGSExtract/wgsextract-cli/main/install.sh | sh

# Put the launcher on PATH, then check your setup
$ export PATH="$PWD/wgsextract-cli:$PATH"
$ wgsextract deps check

# See available commands
$ wgsextract help

CLIAutomation first

LocalRuns on your machine

PixiReproducible tools

WGSExtract CLI desktop app showing command-line workflow output.

A practical reference site, not just a splash page.

Use the pages below as a map for installing the tool, understanding WGS file types, and running common genome workflows safely.

The current release is v0.6.6. It adds native Linux ARM64, Oxford Nanopore detection with Sniffles and optional Clair3 calling, CpG methylation pileups, Y-STR panels, queryable variant tables, result manifests (--json) and easier help. Earlier v0.6.x work added native Windows tools and GATK acceleration, more microarray and AADR exports, resource preflight, and one-command developer setup. See GitHub Releases for full notes.

Install

Install the standalone app or use Pixi directly

Use the standalone macOS/Linux installer, the native Windows installer, or one-command developer setup for a source checkout. Linux ARM64 is supported natively.

Read the install guide

CLI reference

Command groups and recipes

Learn the major command families for info, BAM/CRAM, extraction, VCF calling, annotation, lineage, alignment, FASTQ QC, references, and fake data.

Open the CLI guide

Workflows

Go from a goal to commands

Follow recipes for microarray simulation, Y-DNA and mtDNA extraction, variant calling, FASTQ to BAM, storage conversion, and testing.

Pick a workflow

WGS guide

Learn whole genome concepts

Get a friendly explanation of whole genome sequencing, coverage, references, variants, file types, read technologies, and interpretation limits.

Read the WGS guide

Reference

Glossary and safety notes

Look up common terms, file extensions, external tools, privacy considerations, and troubleshooting tips for long-running genome jobs.

Open the reference