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seqhiker
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seqhiker
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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/ <table> <tr> <td width="50%"> <a href="docs/_static/seqhiker_screenshot_1.png"> <img src="docs/_static/seqhiker_screenshot_1.png" alt="seqhiker screenshot 1" width="100%"> </a> </td> <td width="50%"> <a href="docs/_static/seqhiker_screenshot_2.png"> <img src="docs/_static/seqhiker_screenshot_2.png" alt="seqhiker screenshot 2" width="100%"> </a> </td> </tr> <tr> <td width="50%"> <a href="docs/_static/seqhiker_screenshot_3.png"> <img src="docs/_static/seqhiker_screenshot_3.png" alt="seqhiker screenshot 3" width="100%"> </a> </td> <td width="50%"> <a href="docs/_static/seqhiker_screenshot_4.png"> <img src="docs/_static/seqhiker_screenshot_4.png" alt="seqhiker screenshot 4" width="100%"> </a> </td> </tr> </table> # 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.
