seqhiker

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Genome browser 🧬👀🚀

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# seqhiker

Genome browser for FASTA, annotation, BAM, and VCF files, with a stacked genome comparison view.

It is heavily inspired by Artemis/ACT. The aim is easier install and use,
keeping key functionality of Artemis/ACT, but I have added extra
features. It was developed with substantial coding assistance from
[OpenAI Codex](https://openai.com/codex), which helped with implementation,
tests, documentation, and benchmarking under human direction and review.

Documentation: https://seqhiker.readthedocs.io/en/

# Quick Start

## Install

1. Go to the [latest release](../../releases/latest).
2. Download the build for your operating system and architecture.
3. Open the app.

## View genomes

1. Launch `seqhiker`.
2. Drag and drop your files into the window.

A sequence file must be included, for example FASTA, GenBank, EMBL, or a GFF3 file with embedded sequence.

Typical files:
- FASTA
- GenBank
- EMBL
- GFF3
- BAM (sorted and indexed)
- VCF

`seqhiker` will load the files and open the matching genome view.

A standalone GFF3 with an embedded `##FASTA` section is treated as a sequence-bearing genome file.

You can also switch to `Comparison view` in the toolbar and add genomes one-by-one to compare them.

seqhiker

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