cyanea/alignment-viewer
WASM PopularInteractive BAM/SAM alignment viewer with pileup visualization, variant highlighting, and coverage plots. Zero server needed.
Overview
Alignment Viewer renders BAM/SAM alignment data directly in the browser. Navigate to any genomic region, see read pileups with mismatches highlighted, and inspect coverage depth — all powered by WebAssembly with no backend required.
Features
- Pileup view — Reads stacked by position with mismatches, insertions, and deletions color-coded.
- Coverage track — Real-time coverage depth histogram above the pileup.
- Variant highlighting — SNPs and indels are automatically highlighted against the reference.
- Region navigation — Jump to coordinates (e.g.,
chr1:1,000,000-1,001,000) or search by gene name. - Read details — Click any read to see mapping quality, CIGAR string, flags, and tags.
- Split view — Compare two BAM files side-by-side for tumor/normal or before/after analysis.
How It Works
BAM files are indexed client-side using cyanea-io’s BAM parser compiled to WASM. The viewer fetches only the byte ranges needed for the current viewport, so even multi-gigabyte files are navigable. Alignment operations use cyanea-align for local realignment and mismatch detection.
Use Cases
- Variant validation — Visually confirm variant calls by inspecting the supporting reads.
- Pipeline debugging — Check alignment quality without downloading IGV or setting up a server.
- Presentations — Embed a live alignment view in talks or notebooks.
- Privacy-sensitive data — View clinical alignments without uploading to any third-party service.