The Seqhiker’s Guide

seqhiker is an interactive genome browser for viewing reference sequence, annotations, BAM alignments, VCF variants, and whole-genome comparison layouts.

This documentation is a quick user guide. Start here if you want to install the app, open your files, and begin exploring a genome.

Quick start

1. Install the latest release.

2. Open seqhiker.

3. Drag and drop your files into the window.

A sequence file must be included. This can be:

• FASTA

• GenBank

• EMBL

You can then add:

• GFF3 annotations

• BAM files

• VCF files

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

For more detail, see:

Contents

• Install
  • Download
  • macOS
  • Windows
  • Linux
• Supported files
  • Sequence files
  • Annotation files
  • Compressed files
  • Read alignment files
  • Variant files
  • Download by accession
  • Comparison session files
  • Typical combinations
• Navigation
  • Mouse and wheel
  • Trackpad
  • Toolbar controls
  • Selection
  • Temporary save/jump views
  • Contig menus
• Contig Actions
  • Opening the menu
  • Available actions
  • Browser mode behavior
  • Comparison view behavior
  • Notes
• Theme Editor
  • Opening the editor
  • What you can edit
  • Theme management
  • Import and export
  • Notes
• Comparison view
  • Opening comparison view
  • Loading genomes
  • Layout
  • Core interactions
  • Region selection
  • Search and Go
  • Zoomed-in detail
  • Saving and loading sessions
  • Temporary view slots
  • Export
• Genome and annotation tracks
  • Genome track
  • Annotation track
  • Multi-exon features
  • Interaction
• Reads track
  • Detailed and summary views
  • Read views
  • BAM display
  • Pileup logo
  • Soft-clipped bases
  • Read details
• VCF track
  • Supported variant files
  • Layout
  • Rendering
  • Interaction