# Supported files

## Sequence files

A sequence file is required. Supported sequence inputs are:

- FASTA
- GenBank
- EMBL
- GFF3 with embedded sequence (`##FASTA`)

Without a sequence file, `seqhiker` cannot open a genome view.
If a file with sequence and annotation is used, the annotation will be loaded
together with the sequence.

This means a standalone GFF3 file with an embedded FASTA section behaves like a GenBank or EMBL file: it loads both sequence and annotations from one file.

These same sequence inputs can also be added to comparison view.

## Annotation files

Supported annotation input:

- GFF3 (with or without sequence)

If a reference is already loaded and you then drop a GFF3 with embedded sequence, `seqhiker` checks that the embedded sequence matches the loaded genome. If it matches, the file is treated as annotation input and the annotations are merged into the current genome instead of replacing it.

In comparison view, dropping a FASTA together with its matching GFF3 loads one comparison genome with annotations.


## Compressed files

Sequence/annotation files can be uncompressed, or compressed with any of gz, xz, zstd, bzip2.

## Read alignment files

Supported read alignment input:

- BAM

BAM files must be:

- coordinate-sorted
- indexed, with .bam.bai or .bai present

## Variant files

Supported variant input:

- VCF
- compressed VCF (`.vcf.gz`, `.vcf.xz`, `.vcf.zst`)

Variant files are loaded into a shared `VCF` browser track with one row per sample.

## Download by accession

`seqhiker` can also download genome data by accession from inside the app.

Use this when you want to fetch a reference and annotations without preparing local files first. The downloaded data can be loaded into either:

- browser view
- comparison view

depending on which view is currently active.

## Comparison session files

Comparison view can save and load self-contained comparison session files:

- `.seqhikercmp`

These store the loaded comparison genomes and the comparison state so you can reopen the session later.

## Typical combinations

Common ways to use `seqhiker`:

- FASTA + GFF3
- GFF3 with embedded sequence
- FASTA + BAM
- FASTA + VCF
- FASTA + GFF3 + VCF
- FASTA + GFF3 + BAM
- FASTA + GFF3 + BAM + VCF
- GenBank alone
- EMBL alone
- comparison of multiple FASTA/GFF3 genomes loaded one-by-one