Run from the GUI

Download the latest desktop GUI build (Windows or macOS) from Downloads.

A lightweight desktop GUI wraps the same pipeline logic with a simple form.

Basic panel

Input FASTQ: your reads file (gzipped is OK)
Output folder: where a run folder will be created
Output prefix: sample name (defaults to input basename)
MAFFT threads: how many CPU threads MAFFT can use

Advanced panel (collapsible)

The advanced panel exposes options that are useful for power users, but not required for most runs:

Subsample size
Minimum mean Q
Random seed
Override MAFFT executable (useful on Windows when MAFFT is a .bat)
Toggle BLAST integration (if BLAST+ + DB are available)
Force re-run / ignore existing intermediates

Recommended folder layout (project-local tools)

Place third-party tools under a project-local bin/ folder:

bin/
  # Windows
  mafft-win/mafft.bat
  blastn.exe
  makeblastdb.exe

  # macOS (either system-installed tools OR local binaries)
  mafft-mac/mafft.bat
  blastn
  makeblastdb

And your reference DB under:

blast/
  HmtG_database_PacBio.*

The GUI can auto-detect these paths if you keep this layout.