ChromaZ — Contig Alignment Viewer & Chromatogram Editor

Languages: English | Русский

ChromaZ is a cross-platform desktop C++/Qt6 application for contig assembly, Sanger sequencing chromatogram visualization, multiple sequence alignment, and bioinformatics analysis of nucleotide and amino acid sequences.

Pre-compiled standalone installers are available directly in the root of this repository:

• Debian / Ubuntu: Download ChromaZ_Linux_Install_VERSION_amd64.deb.
• Windows: Download ChromaZ_Windows_Install_VERSION.exe.
• macOS: Download ChromaZ_macOS_Install_VERSION.dmg

• 7+ Independent Alignment Algorithms:
  • OLC / CAP3 (Sanger Default) — Vector NTI ContigExpress style overlap assembly with zero penalty for 5'/3' overhangs.
  • Affine-Gap Block (Gotoh) — Semi-global alignment with separate gap-open and gap-extension penalties.
  • Needleman-Wunsch — Strict global alignment.
  • Smith-Waterman — Local alignment targeting regions of maximum identity.
  • BLAST (Seed & Extend) — Accelerated $k$-mer search with extension along the optimal diagonal.
  • Banded DP — Banded dynamic programming for long reads.
  • Wavefront Alignment (WFA) — Stepwise wavefront error-expansion algorithm.
  • Internal Progressive Clustal — Built-in progressive multiple sequence alignment (MSA) without external CLI dependencies.
• Auto-Contig & Reference Support: Automatic seed selection based on the most representative read, or custom reference sequence loading (FASTA/GenBank).
• Reverse Complement Detection (Auto RC): Automatic strand orientation and alignment for complementary reads ([RC]) with manual toggle option.

• Four-Color Chromatogram Plot: Trace visualization for Sanger sequencing files (.ab1 and .scf) using standard base colors (A — green, C — blue, G — black/yellow, T — red).
• Phred Quality Scores: Color-coded quality visualization per base (Green $Q \ge 30$, Yellow $Q \ge 20$, Red $Q < 20$).
• Quality Trimming (Trim Low QC): Automated low-quality end-trimming based on Phred thresholds.
• Nucleotide Coordinates & Ruler: 1-based nucleotide position numbering displayed above each read, consensus, and reference (excluding gap columns).

• 6 Open Reading Frames: Translation and visualization of forward (+1, +2, +3) and reverse (-1, -2, -3) frames for protein-coding regions.
• Independent ORF A and ORF B Toggles:
  • ORF A: Toggle 6-frame translation display for the top Reference / Auto-Contig sequence.
  • ORF B: Toggle 6-frame translation display for the Consensus sequence.
• Genetic Code Tables: Support for Standard Code (Human), Vertebrate Mitochondrial, and Bacterial/Plant Plastid tables.
• IUPAC Consensus: Ambiguous base calculation (R, Y, S, W, K, M) for mismatched positions across reads.

• Keyboard Sequence Editing: Direct base substitution (A, C, G, T, N, -), insertion, and deletion with automatic trace coordinate recalculation.
• Full Undo / Redo: Multi-step history stack (Ctrl+Z / Ctrl+Y or Ctrl+Shift+Z) up to 100 actions.
• SNP Navigation: Single Nucleotide Polymorphism detection with quick jumping controls (◀ SNP / SNP ▶).
• Fast Sequence Search: Substring match highlighting with automatic viewport auto-scrolling.
• Drag & Drop: Track reordering via drag-and-drop and direct file loading onto the viewer.

• Copy Selection as Image: Copy selected chromatogram segments along with trace peaks directly to the clipboard as PNG graphics.
• FASTA Export: Export generated consensus sequence.
• PDF Export: Multi-page PDF report generation with configurable bases per line.
• PNG Export: Save current alignment view as high-resolution raster images.
• .ChromaZ Projects: Save and load complete workspace states (strand orientations, gaps, edits, and undo history) in JSON format.

• C++17 compliant compiler (GCC 9+, Clang 10+, MSVC 2019+)
• CMake 3.16+
• Qt 6.x (Core, Gui, Widgets, Test modules)

git clone [https://github.com/your-username/ChromaZ.git](https://github.com/your-username/ChromaZ.git)
cd ChromaZ
mkdir build && cd build
cmake src/.. && make -j$(nproc)
./ChromaZ

This project is licensed under the MIT License. See the LICENSE file for details.