FiberBrowser 3.0.1

FiberBrowser 3.0.1 bundles FiberHMM 3.0.2 and requires
fiberhmm[consensus]>=3.0.2,<4.

Fixed

• The guided tour starts on first launch. After declining the offer to
  restore a session (or on a first launch with no genome downloaded), the tour
  could stop at its first step with "load a BAM or BigBed with Open". The tour
  tab no longer loads a start-up genome of its own, so it no longer waits for
  the main window's genome download; it opens the demo at once, without a
  reference sequence if the demo's genome is still downloading. If the demo
  cannot be opened, the tour asks again and then says why it can't start.
• DddA QC grades against a somatic DddA control. FiberHMM 3.0.2 replaces
  the DddA reference that fiberhmm-qc compares samples with: the packaged
  one came from a sperm DAF-seq sample, so normal DddA libraries failed the
  signal-rate and periodicity grades. Re-run Data quality (QC) on DddA
  datasets; QC reports made with earlier versions graded DddA against the
  wrong control. Footprint calls, DddB and Hia5 grades are unchanged.

Downloads

• Mac (Apple silicon, macOS 14+): FiberBrowser-3.0.1-arm64.dmg (signed and notarized)
• Windows 10/11: FiberBrowser-3.0.1-Setup.exe, or FiberBrowser-3.0.1-windows-portable.zip
• Python: pip install fiberbrowser==3.0.1

Checksums are in SHA256SUMS.txt. Installing over 3.0.0 keeps your settings, saved sessions and Library.

FiberBrowser 3.0.0

FiberBrowser 3.0 is released together with FiberHMM 3.0, the third
generation of the FiberHMM family, and requires it:
fiberhmm[consensus]>=3.0,<4 (installed with FiberBrowser). Browsing works
without FiberHMM; footprint classes, chemistry detection, consensus BAM
export, DAF-seq runs and re-run advisories need it.

Nanopore Hia5 and DddB users: re-call your BAMs. FiberHMM 3.0 ships new
Nanopore Hia5 and DddB models. Re-call Nanopore Hia5 and DddB BAMs made with
FiberHMM 2.x using FiberHMM 3.0 and reload them. The Library marks BAMs that need it (Needs re-run)
and can re-call DAF-seq runs made in FiberBrowser. See the
FiberHMM 3.0.0 changelog.

What 3.0 includes

• Supported: SV display and splits, the insertion lens and Identify (with the bundled fly TE library and
  Dfam downloads), and the Variants panel (SNPs, local read-supported allele patterns, SVs, splits by allele or
  haplotype).
• Preview, on by default (Show preview features, Settings → Reads & Display): insert-expanded
  (alt-allele) panels. Each way into them has a Preview badge and a Known limitations note that says what
  graduates it. With previews off, a session that uses them keeps everything and offers to turn them on. The
  Footprint classes section of the Footprints panel carries a Preview badge but stays available with previews
  off. See What 3.0 includes.
• NFRs and Synchronise regions (its own rail icon) are in every build, independent of the preview switch.
  Sessions and preferences from earlier 3.0 builds open unchanged.
• The Variants panel has a sequence-variant icon on the rail.
• The guided tour (58 steps) has a Variants section on a second bundled demo (H1 PacBio Fiber-seq around a
  heterozygous 7,471-bp insertion on chr1 whose insert carries a CTCF-footprinted NFR): SNPs in view, a split by
  haplotype (HP tags), the SVs tab and the insert expanded. The user guide and the tutorial cover it.

Downloads

File	For
FiberBrowser-3.0.0-arm64.dmg	macOS on Apple silicon (signed and notarized)
FiberBrowser-3.0.0-Setup.exe	Windows 10 2004+ or 11, x64 (runs in WSL 2). Unsigned, so SmartScreen asks you to confirm.
FiberBrowser-3.0.0-windows-portable.zip	The same Windows app without the installer (run Install.cmd)
FiberBrowser-3.0.0-wsl-amd64.tar.gz	The WSL distro on its own, for wsl --import
fiberbrowser-3.0.0 wheel / sdist	pip install fiberbrowser (Linux, macOS, WSL)

The desktop apps bundle FiberHMM 3.0.1. Checksums are in SHA256SUMS.txt.

The full list of changes is in the CHANGELOG.