Supported files

Sequence files

A sequence file is required. Supported sequence inputs are:

  • FASTA

  • GenBank

  • EMBL

  • GFF3 (with sequence)

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.

Annotation files

Supported annotation input:

  • GFF3 (with or without sequence)

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

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 is then loaded into the same browser view as manually dropped files.

Typical combinations

Common ways to use seqhiker:

  • FASTA + GFF3

  • FASTA + BAM

  • FASTA + GFF3 + BAM

  • GenBank alone

  • EMBL alone